Problems with my 2nd Gen

I'm having a lot of problems with the bike ever since I took it to get the Cabs and Valves done.

I took the bike to a local VF/VFR guru to get my carbs overhauled, and to inspect the valve clearances. He had the bike for 3 days and called me to say the bike was ready for pickup. He said the Carbs were good and only had just a bit of Varnish in the bowls. Intake Valves had a tad too much clearance and the Exhaust had a tadd too little clearance. They were adjusted to spec and everything else checked ok.

I rode the bike home from his place which is about 62kms.

When I got home the rad cap was spewing coolant. After it cooled down I refilled the system and after ensuring the rad cap was secure, took the bike for a nice Hour long ride and everything seemed fine. When I got home from that ride I noticed the Stator cover gasket was leaking oil. (later, the guy who worked on my bike admitted he removed the stator by accident. Something about being used to the VF’s where you needed to do that to turn the motor to check valve clearances) So I spent the next week flushing the coolant system and getting that leak fixed.

While I was running the bike and burping the coolant system I noticed black smoke coming from the left exhaust pipe. The idle had a bit of a stumble to it too. I put it out of my head and got working on that stator cover. As I was lying beside the bike scraping old gasket off I looked up and noticed one of the carb boots was wet. I ran my hand along the bowl of the front left carb and my hand came back wet with gas. I immediately turned the Petcock to OFF and contacted the guy who worked on my bike. He agreed to come by on Monday to look at the bike. The days before he came by I got the Stator cover sealed with Honda Bond and (as per his request) drained that one Float bowl.

I also removed the spark plug from the front Left cylinder and sprayed the tip with carb cleaner. I then put some motor oil on the threads and re-installed it.

Monday comes around, and so does he. Of course the carbs aren’t leaking fuel. I started the bike and rode it around my court and there was grey/bluish smoke coming from the Left Pipe this time. He then checks the float bowl levels and he says they are all pretty close. I take the bike for a 15 minute ride around town and the bike performs well. No more smoke. No leaking carbs. Man goes home. I cover bike.

This morning, I decided to take it to work.
I haven't started it since that Monday when I went for that 15minute ride. The bike has been sitting in the driveway with the cover on it.

I took the cover off of it and put my hand under the carbs and ran my fingers on them. They were wet with gas. (definitely gas)

I tried starting the bike and with full choke (and only full choke) it started up but the idle was very low. After about a minute of idling the bike died. I was then unable to start it no matter how much (or how little) choke I gave it. Eventually I got it started with no choke and by cracking the throttle open while starting it. The bike would die if I didn't give it any throttle.

I took it for a quick spin and it was stumbling and sputtering all over the RPM band. It would bog if I gave it too much throttle. I couldn't see any smoke coming from the exhaust while I was riding.

After about 2 minutes of riding the bike started to behave and the sputtering and stumbling went away. I pulled into my drive way and put the bike on the kickstand and the bike immediately died. It was again very difficult to start.
I can see the fuel leaking from the carbs onto the cylinder head.
I just e-mailed the guy and asked him to come get my bike to fix it, cause it was running fine before I took the bike to him.

Any ideas as what the problem could be?

Sounds like it's still flooding out. Spark plugs are probably now getting fouled too which is not helping matters.

Guru you say?

Could be a number of things going on.

[image: View Post]FotoMoto, on 09 September 2010 - 10:40 AM, said:

Sounds like it's still flooding out. Spark plugs are probably now getting fouled too which is not helping matters.


Yes....they are brand new too. I'll probably have to pul lthem when this is all resolved to clean them. :dry:

[image: View Post]SEBSPEED, on 09 September 2010 - 10:50 AM, said:

Guru you say?

Could be a number of things going on.


Yea. I would usually say "Guru" cause he has worked on hundreads of VF/VFR's and knows a lot about them. But at the end of the day people are only human and mistakes happen.....though it seems like a lot of mistakes were made on my bike. :angry:

Did he really clean the carbs, or just open one up and identify some varnish in the bowl and leave it at that?

The float needle on that one carb may be stuck open... by .... some varnish. If varnish is in the bottom of the bowls, then it is everywhere else also.

You can't just look in the bowl to determine if a carb is clean--must remove jets and poke steel wire thru them to ensure they are open. Varnish in the starting circuit (choke) will make a bike hard to start when the engine is cold. Varnish in the slow jet will make a bike not want to idle. Varnish on the needle will cause erratic throttle response and control.

Check the fuel rail tees, maybe he cracked one when he was "cleaning".

Turn your petcock off when you're not riding. If it is still leaking past, then replace the rubber petcock seal.

[image: View Post]kennybobby, on 09 September 2010 - 07:36 PM, said:

Did he really clean the carbs, or just open one up and identify some varnish in the bowl and leave it at that?

The float needle on that one carb may be stuck open... by .... some varnish. If varnish is in the bottom of the bowls, then it is everywhere else also.

You can't just look in the bowl to determine if a carb is clean--must remove jets and poke steel wire thru them to ensure they are open. Varnish in the starting circuit (choke) will make a bike hard to start when the engine is cold. Varnish in the slow jet will make a bike not want to idle. Varnish on the needle will cause erratic throttle response and control.

Check the fuel rail tees, maybe he cracked one when he was "cleaning".

Turn your petcock off when you're not riding. If it is still leaking past, then replace the rubber petcock seal.


Thanks for the response KB. :fing02: Good info.

The leak seems to be coming from (to the best of my poking an proding around the carbs) the left front Carb....around the float bowl. It doesn't look wet above that area.

My question, if the float is stuck open, will the fuel leak out the the carbs somewhere? (float bowl seal) or will it just leak into the cylinder?

[image: View Post]slowbird, on 09 September 2010 - 09:29 PM, said:

The leak seems to be coming from (to the best of my poking an proding around the carbs) the left front Carb....around the float bowl. It doesn't look wet above that area.

My question, if the float is stuck open, will the fuel leak out the the carbs somewhere? (float bowl seal) or will it just leak into the cylinder?


If the bowl gasket is intact then the overflow will wash down into the cylinder past the rings and fill up your crankcase with gasoline. Pull the oil filler cap and check the "oil" level--if this has gone on for a while your entire crankcase can get filled and hydrolock the engine. Then when you try to start the motor something expensive will get broken by the intense hydraulic pressure inside the closed crankcase, i.e. don't do it--drain, catch and measure the amount of "oil".

i once drained an 83 vf70 that did this and pulled 3 gallons out of the crankcase! (oil/gas mixed)

If the bowl gasket are old, flat or broken then the bowl overflow will wet the bowl area such as you described.

But check you crankcase because if the #2 carb is not shutting off, then the others may be dripping also but their gaskets might be intact...

[image: View Post]kennybobby, on 09 September 2010 - 09:57 PM, said:

[image: View Post]slowbird, on 09 September 2010 - 09:29 PM, said:

The leak seems to be coming from (to the best of my poking an proding around the carbs) the left front Carb....around the float bowl. It doesn't look wet above that area.

My question, if the float is stuck open, will the fuel leak out the the carbs somewhere? (float bowl seal) or will it just leak into the cylinder?


If the bowl gasket is intact then the overflow will wash down into the cylinder past the rings and fill up your crankcase with gasoline. Pull the oil filler cap and check the "oil" level--if this has gone on for a while your entire crankcase can get filled and hydrolock the engine. Then when you try to start the motor something expensive will get broken by the intense hydraulic pressure inside the closed crankcase, i.e. don't do it--drain, catch and measure the amount of "oil".

i once drained an 83 vf70 that did this and pulled 3 gallons out of the crankcase! (oil/gas mixed)

If the bowl gasket are old, flat or broken then the bowl overflow will wet the bowl area such as you described.

But check you crankcase because if the #2 carb is not shutting off, then the others may be dripping also but their gaskets might be intact...


Thanks KB. I'll check the Crank Case level first.

I checked the crankcase. It's still on the level. So if gas went in it hasn't shown on the dipstick.

Petcock to Off and the leaks stop around the carbs.

I took the carbs out.....opened up all 4 float bowls. Cleaned the Jets and the float seats and everything in there. The floats look like the move freely. Nothing is binding them up.

[image: Posted Image]

I hope I free'd something up with my cleaning and this problem goes away. I also hope I don't need to order any parts.

I pulled all 4 plugs. The 2 left ones were wet and fouled. Right ones looked normal.

The carbs weren't perfectly clean inside. I don't know if the float bowls can accumulate this much crap in the bowls from a week.
[image: Posted Image]

The guy who worked on my bike finally called. Asked me to check the Airbox for oil. It was pretty clean when I got in there.

Everything clean and re-installed. Bowls re-attached.

Carbs went on easier than taking them off.

Bike took some cranking to start. I tried with and without choke. It started with about 3/4 choke. Slowly the bike started to stumble and die.

I could get the bike started with no choke and by cracking the throttle open. While it was running I sprayed each header pipe with carb cleaner and noticed the front left wasn't evaporating. I pulled that plug and it was wet. I cleaned the plug and tested it by leaving it on the wire and putting it near the frame. I could see a tiny spark when cranking the motor.

I pulled the other front plug and it was BLACK. I cleaned it, made sure the gap was good....swapped the plugs and started the bike. (No choke) It started no problems....seems to run good.

I'm guessing I need to tune or synch the carbs somehow?

[image: View Post]slowbird, on 11 September 2010 - 12:42 PM, said:

I checked the crankcase. It's still on the level. So if gas went in it hasn't shown on the dipstick.

Petcock to Off and the leaks stop around the carbs.

I took the carbs out.....opened up all 4 float bowls. Cleaned the Jets and the float seats and everything in there. The floats look like the move freely. Nothing is binding them up.

[image: Posted Image]

I hope I free'd something up with my cleaning and this problem goes away. I also hope I don't need to order any parts.

I pulled all 4 plugs. The 2 left ones were wet and fouled. Right ones looked normal.

The carbs weren't perfectly clean inside. I don't know if the float bowls can accumulate this much crap in the bowls from a week.
[image: Posted Image]

The guy who worked on my bike finally called. Asked me to check the Airbox for oil. It was pretty clean when I got in there.

Everything clean and re-installed. Bowls re-attached.

Carbs went on easier than taking them off.

Bike took some cranking to start. I tried with and without choke. It started with about 3/4 choke. Slowly the bike started to stumble and die.

I could get the bike started with no choke and by cracking the throttle open. While it was running I sprayed each header pipe with carb cleaner and noticed the front left wasn't evaporating. I pulled that plug and it was wet. I cleaned the plug and tested it by leaving it on the wire and putting it near the frame. I could see a tiny spark when cranking the motor.

I pulled the other front plug and it was BLACK. I cleaned it, made sure the gap was good....swapped the plugs and started the bike. (No choke) It started no problems....seems to run good.

I'm guessing I need to tune or synch the carbs somehow?


Good news on the crankcase then.

Might want to get a new fuel filter or add a second one (clear in-line type to see what's coming out of your tank).. is your tank rusty inside? Any little rust particles getting thru will give you problems such as not starting on choke, overflow/leaking carb bowls, etc. The tiny orifices in the pilot and starting circuits can easily clog.

Nice pictures, did you take all the jets out to clean while it was opened up, also clean the little screens above the inlet float needle, etc. it's so much more fun to clean "Everything in there" the first time than to have to go back in a second time...

Don't run dirty old bad fuel back thru into clean carbs. Make sure the tank is not rusty and causing your carb issues. If it is rusty, take it to a radiator shop and let them boil it out, then redcoat the interior. Rod out all the metal tubes in the tank, put 2 new fuel filters inline, only then put fresh gas into your absolutely spotless and totally clean carbs (meaning each and every circuit component has been inspected and known to be clean, i.e. the inlet, choke, idle/pilot,main circuits). If you try to take short cuts the bike will never run properly and you will never be happy with the results...BTDT

Tank is clean from what I can see inside. It does look coated though.

First thing when I got the bike was drain the old fuel, and change the Fuel filter.

When I had the float bowls off I did remove the jets that the repair manual said I could remove. I made sure they were all clear and I could see through them.

I removed the float needle and cleaned it. I also removed the float seat and cleaned that and the filter.

Just now I sStarted the bike and I started spraying carb cleaner on the 2 front header pipes, back and forth.

The Front Left cylinder definitely doesn't warm up as fast as the other 3.

I guess the carbs need to be synch'd?

[image: View Post]slowbird, on 11 September 2010 - 01:31 PM, said:

Tank is clean from what I can see inside. It does look coated though.

First thing when I got the bike was drain the old fuel, and change the Fuel filter.

When I had the float bowls off I did remove the jets that the repair manual said I could remove. I made sure they were all clear and I could see through them.

I removed the float needle and cleaned it. I also removed the float seat and cleaned that and the filter.

Just now I sStarted the bike and I started spraying carb cleaner on the 2 front header pipes, back and forth.

The Front Left cylinder definitely doesn't warm up as fast as the other 3.

I guess the carbs need to be synch'd?

The number 2 carb is the reference for synching, and it is the cylinder that is not working right. My guess is that the 1,3,4 carbs have been adjusted way open to get the bike to run or idle and the #2 is closed off, hence not heating up.

You can look down the venturis at the position of the butterfly valve--they should all have about the same gap showing. One way to do a quick check is to use a couple of equal size drill bits, say 1/4". Open the throttle and put a 1/4" bit under the #2 butterfly valve to hold it open (tape it or put a lanyard so it doesn't drop into your valves if it slips out). Then use another 1/4" bit to check the gap on the butterflys for the 1,3,and 4. If you can easily get to the adjusting screw you could adjust 1,3,4 as needed to match the 1/4" gap on the reference #2--this will get you back into the ballpark and make the bike rideable. But first---

What about the pilot screws--did you pull them and check the ends for damage, clean them, then install gently all the way in, then back them out 2-1/2 turns?

Now start it and set the idle speed using the master idle adjustment screw to about 1200 rpm. If you want to tweak the pilot screws to adjust the idle mixture there is a procedure in the manual based upon changes in the engine speed, etc., but it can be ridden like this for the weekend and mess with it later--you should go ride and run some fuel through those bad boys...

Hmmm....well I didn't touch the pilot screws at all. To be honest I didn't even notice them :mellow: oops.

I just took it for a ride. Bike feels good. Not great....but good. Seems to stutter a bit through the low and mid range. Pulls hard after that.

I can tell it's just not running right.

All cylinders are definitely firing, but #2 might be running a bit rich. Using my little laser thermometer I can see the #2 header pipe is not running as hot as the other 3.

Do I have to remove the carbs to adjust those pilot screws?

[image: View Post]slowbird, on 11 September 2010 - 05:17 PM, said:

Hmmm....well I didn't touch the pilot screws at all. To be honest I didn't even notice them :mellow: oops.

I just took it for a ride. Bike feels good. Not great....but good. Seems to stutter a bit through the low and mid range. Pulls hard after that.

I can tell it's just not running right.

All cylinders are definitely firing, but #2 might be running a bit rich. Using my little laser thermometer I can see the #2 header pipe is not running as hot as the other 3.

Do I have to remove the carbs to adjust those pilot screws?

Maybe they still had the anti-tamper caps on them and you didn't see em?

No removal--you can get to them from the sides. They put caps over them at the factory--most older bikes have had the caps pulled off or drilled out. If you have the honda manual there will be pictures of it. There is a small spring, oring and washer in there so be careful when you pull them out and squirt a shot of carb cleaner. Don't overtighten at all or they can be damaged.

Be sure to gently screw them in first and count the number of turns to see how far out they already are. Stock on a 700 is 2.5 turns, not sure on the 750--we didn't get that version in the us due to the extra help Harley tax on bikes over 750 cc.

The idle speed will change when you start messing with the pilots also, so you'll have to readjust the master idle, etc.

Chances are the pilot screw on #2 has been backed way out with respect to the other cylinders--especially since it is the easiest one to access...

So you are recommending I remove the Pilot screws and spray in there with some carb cleaner?

Do I need just a screwdriver to get the pilot out?

[image: View Post]slowbird, on 11 September 2010 - 09:55 PM, said:

So you are recommending I remove the Pilot screws and spray in there with some carb cleaner?

Do I need just a screwdriver to get the pilot out?

Yes i would recommend that AFTER you first screw them in gently to count the number of turns and determine where they currently are set.

The US bikes had caps over the screws--anti-tamper. The 750 was probably a Canadian bike, may not have caps, may just need a screwdriver. Here's a factory manual page for a 700, hope it helps a little. If they have caps, or maybe cover plugs, then those will need to be removed. Go take a look to see if you can find them.

[image: Posted Image]

My service manual has a similar procedure.

My question is if (before I remove the Pilot Screws) I count the amount of turns and it's for example 2.5 turns, but the service manual says: initial opening: 1 7/8 turns

Am I putting them back to the position they were before i removed them, or the Initial Opening position mentioned in the manual?

[image: View Post]slowbird, on 11 September 2010 - 11:09 PM, said:

My service manual has a similar procedure.

My question is if (before I remove the Pilot Screws) I count the amount of turns and it's for example 2.5 turns, but the service manual says: initial opening: 1 7/8 turns

Am I putting them back to the position they were before i removed them, or the Initial Opening position mentioned in the manual?


[image: Posted Image]

I would recommend you put them to the Initial Opening position found in the service manual for your model.

The reason you want to count the current position is to gain insight into why it is running bad--have they been adjusted before, and if so how much. Also, if for some strange reason the bike won't run with the stock settings you could always go back to these recorded settings where it is known to run, albeit poorly.

Thanks for all the useful info KB. Here is where I am at now:

I think the confusion about when to sync and when not to sync, and when you are supposed to mess with the pilot screws is part of the reason this guy who worked on my bike is doing such a poor job. I've been given the impression that he didn't touch the pilot screws or synch the carbs. He just cleaned the carbs a little and checked that all 4 float bowls had the same amount of fuel coming out of them. (he said it was close)

He attaches a tube to the float bowl drain and drains each bowl into a measuring cup and makes sure they are all the same. ???

When I had the carbs out I cleaned everything. I removed the jets and made sure they were clean. I also cleaned the little filters in the float valve guide area.

I went out to the bike this morning and the carbs were wet with gas again. They seem to seep fuel after sitting overnight.
I run my finger along the seem where the float bowl meets the carb body (front left carb) and it comes back wet with gas. I guess I need new float bowl o-rings?

I pulled the front two plugs:

The front left plug looked like this:
[image: Posted Image]

^^ This is the cylinder that the header pipe doesn't heat up as much or as fast as the others.


The front right plug looked like this:
[image: Posted Image]

I cleaned and re-installed them both. Started up the bike. It didn't idle great. A little black smoke came out of the exhaust when I revved it.

Took it for a spin and it still suffering low to mid range. Idle feels rough.

:frown:

I guess I need to start with the pilot screws? One of them is blocked by the thermostat housing. :angry:

Check your float levels as per the manual.

Anyone who works on any Honda knows there is a plug that you unscrew to get at the crankshaft to check the timing and/or valve clearances.
PLEASE DO NOT EVER GO BACK TO THIS GUY.

As I said on GTAM, pm me if you want help or a second set of eyes.

If you just have a drop or two of fuel on the seam (as opposed to a gushing, dripping leak) then you might slow the leak down using a little grease smeared over the oring, or a very thin layer of some of that brown high tack flexible gasket sealer (not silicone sealer).

i don't remember the size, but you can use a regular round oring of the right diameter and push it into the groove--cheaper than the custom bent ones.

Can you see the heads of the pilot screws or are they plugged? Go ahead and count the turns to close them. If the pilots are way open, then the plugs will foul just as you have shown. Don't worry about carb synch until you solve the pilot issue. There is no need to try to ride it until you know what your settings are--these kind of problems won't heal themselves by trying to be ridden.

Found a couple things that may be adding to my issues:

1. Fuel flow does not stop when you put the Petcock to OFF. Going from ON to RESERVE seems to work. (judging by me being able to switch to reserve when the bike gets low on fuel) But when I disconnect the fuel line from the fuel filter it just flows out and doesn't stop. I managed to plug the hose to prevent all the gas from the lank leaking out.

2. Float is getting gas in it somehow. It drops (sinks) lower than the rest.

[image: View Post]slowbird, on 14 September 2010 - 02:33 PM, said:

Found a couple things that may be adding to my issues:

1. Fuel flow does not stop when you put the Petcock to OFF. Going from ON to RESERVE seems to work. (judging by me being able to switch to reserve when the bike gets low on fuel) But when I disconnect the fuel line from the fuel filter it just flows out and doesn't stop. I managed to plug the hose to prevent all the gas from the lank leaking out.

2. Float is getting gas in it somehow. It drops (sinks) lower than the rest.

You can replace the rubber washer inside the petcock to fix fuel not shutting off.

It sounds like you have a cracked float and it is going to flood out that carb bowl/cylindder--is it the #2 carb that was dripping, or the #4 carb with the black spark plug?

What did you find out about the pilot screw settings?

So here's a quick update:

First off, I don't have a garage or a place to work on the bike. It all has to be done in my driveway and by the time I get off work it's already getting dark. Since the problems began I have had little time to do anything besides pull fairings or check plugs.

I spoke to the guy who worked on my bike and he was as baffled and upset at the situation as I was. After I complained of his work we spoke and I decided to give him a chance to correct his errors. (no charge to me of course)

When he got the bike he found the float with the fuel in it. It had a small crack. He also found the broken Petcock switch. He replaced both parts for me and didn't ask for any $$.

He said he re-checked all the work he did and everything looked ok. He ran a compression test and it came up with 145-155.

I got the bike back from him and it seemed a bit difficult to start when it was cold. I rode it home (60+km's) and once, my GF who was tailing me in her car said she saw a bit of smoke come from the bike when I accelerated hard onto the highway.

The bike STILL has a fuel leak. Even the guy said I should switch the petcock to off and try and park the bike as upright as possible. :rolleyes: (Gee...thanks)

I took the bike to work this morning. It started fine. While the bike was warming up I noticed the exhaust didn't look to good. When I reved it the exhaust was a bit blackish. (there's no smoke when i start riding it though)
I don't know if the choke is creating an overly rich condition, or if any amount of idling is fouling the plugs.

It does have a funny feeling idle, Bike feels good about 75-80% of the time when riding it. Idle feels odd. Also, when i get on the throttle around 4,000rpm it stutters a bit before it pulls hard.

Pilot screws are 2.5 turns out.

When the bike is in neutral and I release the clutch I can hear and feel a slight noise and vibration. Goes away when I pull the clutch in. Not easy to notice. (Bike has always done that.)

Sooooooo that's where I am as of today. Bike runs ok. Leaks a bit of fuel. I don't have anyone local to take my bike to anymore for carb/valve work.

Oh.....one thing to bring up. The previous owner of the bike said that the Airbox was modified and it had a K&N air filter. Now it does have a K&N Air filter. (it's clean) but the airbox is stock and unmodified.

[image: View Post]slowbird, on 17 September 2010 - 10:01 AM, said:

So here's a quick update:

First off, I don't have a garage or a place to work on the bike. It all has to be done in my driveway and by the time I get off work it's already getting dark. Since the problems began I have had little time to do anything besides pull fairings or check plugs.

I spoke to the guy who worked on my bike and he was as baffled and upset at the situation as I was. After I complained of his work we spoke and I decided to give him a chance to correct his errors. (no charge to me of course)

When he got the bike he found the float with the fuel in it. It had a small crack. He also found the broken Petcock switch. He replaced both parts for me and didn't ask for any $$.

He said he re-checked all the work he did and everything looked ok. He ran a compression test and it came up with 145-155.

I got the bike back from him and it seemed a bit difficult to start when it was cold. I rode it home (60+km's) and once, my GF who was tailing me in her car said she saw a bit of smoke come from the bike when I accelerated hard onto the highway.

The bike STILL has a fuel leak. Even the guy said I should switch the petcock to off and try and park the bike as upright as possible. :rolleyes: (Gee...thanks)

I took the bike to work this morning. It started fine. While the bike was warming up I noticed the exhaust didn't look to good. When I reved it the exhaust was a bit blackish. (there's no smoke when i start riding it though)
I don't know if the choke is creating an overly rich condition, or if any amount of idling is fouling the plugs.

It does have a funny feeling idle, Bike feels good about 75-80% of the time when riding it. Idle feels odd. Also, when i get on the throttle around 4,000rpm it stutters a bit before it pulls hard.

Pilot screws are 2.5 turns out.

When the bike is in neutral and I release the clutch I can hear and feel a slight noise and vibration. Goes away when I pull the clutch in. Not easy to notice. (Bike has always done that.)

Sooooooo that's where I am as of today. Bike runs ok. Leaks a bit of fuel. I don't have anyone local to take my bike to anymore for carb/valve work.

Oh.....one thing to bring up. The previous owner of the bike said that the Airbox was modified and it had a K&N air filter. Now it does have a K&N Air filter. (it's clean) but the airbox is stock and unmodified.


Here's what i would do, especially since you don't have a garage to work. Wash and dry the bike well, then pull the fairings, wrap them in newspaper and store them in a closet or attic until you get everything running good. You will likely be needing to access the choke and pilot circuits so might as well get stuff out of your way.

If the choke, aka starting enrichment circuit, is not opening fully when the lever is pulled, then you can experience difficulty in starting when it is cold. Also if the choke plungers are not closing completely when the lever is pushed, then the enrichment circuit is dumping gobs of extra fuel all the time, fuel mileage will be poor and the bike will be running too rich and fouling plugs, etc. You might be able to spray some lube on all the choke linkages to free up the action. You might be able to view them from the sides, but likely will need to remove the tank and airbox to be able to see around the edges of the metal airbox plate. Actuate the choke lever and watch the action at each carb by tracing each linkage one at a time. The thumb lever may be moving on the handlebar but the actual linkages and the choke plunger may not, so check each one to verify all is well.

Did you happen to wrote down the sizes of your pilot jets when you had the carb bowls open? It may be that someone put fatter pilots in there when they added the KN filter, and that may be causing the rich mixture condition. If it were my carbs i would turn the pilots in 1/2 turn down to 2, then run it to see how it feels and if the 4k rpm bogging goes away. You may need to screw in the idle speed adjusting screw when you do this to raise the idle speed. Run it for a few days, if that helped it run better, then turn the pilots in a 1/4 turn and raise the idle as necessary, ride and repeat.

i think your problem will be found in the choke or pilot circuits, but when you had the carbs off did you pull the tops to get to the needle slides? Were the rubber diaphragms okay?

The clutch noise you describe seems normal.