The charging system voltage is OK, the battery load test voltages are good, the alternator resistance values are fine, but the battery still flattens quite quickly.
Now we're looking at the battery leakage rate. This is the current (Amps) the bike draws even though everything is turned off.
Ideally the leakage should be less than 1.2mA, but with an alarm fitted and armed it might marginally higher than that. It might be worth consulting the alarm instructions and seeing what current it draws.
You'll need to set your multimeter to the highest DC Amps range. this is to stop the meter overloading when it's connected. On some models of multimeter you'll need to change which connection the red lead goes to.
When set to read amps, under no circumstances connect the multimeter between the battery terminals, otherwise you could short out the battery, melt the leads and wreck the meter.
1. Disconnect the battery negative (earth) lead.
2. Set to multimeter to the highest DC Amps range.
3. Connect the multimeter between the battery negative terminal and the disconnected negative (earth) lead.
4. Going down one DC Amps range at a time, reduce the range until the reading is sensible. Always start high to protect the meter from overloading.
5. The ideal leak rate should be below 1.2mA, but as mentioned above it may be very slightly higher because of any alarms/immobilisers, but not substantially so.
If the leakage is substantially higher than 1.2mA, try pulling and refitting fuses one at a time and seeing which fuse make the biggest difference to the leakage value when removed. This'll give you a clue as to which circuits are drawing too much current.
If you've replaced the Voltage Regulator/Rectifier and Battery and the charging system voltage is still too low.
If this is the case, then there's a good chance the alternator is failing.
Because the alternator is mounted inside the engine the heat from the engine could affect the insulation on the alternator stator windings. The insulation may even break down between the windings. This typically happens under load and when the engine is hot. You will still get a good output voltage from the R/R, but as the VFR uses a delta wound stator, the alternator will give a much lower AC voltage and much higher AC current.
To check the insulation of the alternator stator coils you'll need to do the following:-
1. Disconnect the R/R connection to the alternator - the one with the 3 yellow wires.
2. Select the resistance (Ohms or Ω) range on your multimeter and touch the two probe ends together. The readout on the multimeter will give you the effective zero reading - so if there is a value shown and your multimeter cannot be zeroed - as many cheaper ones can't be, you'll have to deduct this number from any further measurement.
3. On the three yellow wires coming from the alternator (not the ones from the R/R by accident) measure the resistance between each of the wires in turn, i.e. have one probe on the connection to one yellow wire, then touch the other probe to the connections for the other two yellow wires. So if one probe is one wire 1, place the other probe on wire 2 then 3. Then move the probe from wire 1 and put it on wire 2, then place the other probe on wire 3. That way all combinations are covered.
4. The resistance readings in step 3 should be anywhere between 0.1 Ohm and 1 Ohm - remember to deduct the resistance reading you got in step 2 from the values you saw in step 3.
5. Now test the resistance between each of the yellow wires and earth. There should be no continuity, i.e. infinitely high resistance, between any of the yellow wires and earth.
If the values in step 4 or step 5 are outside the tolerances, then there's a pretty good chance the alternator stator coils are knackered.
I will warn you though, having received further information from Brains, the above procedure may not conclusively prove the alternator stator serviceable or unserviceable. As Brains reminded me, a multimeter doing resistance checks only uses a few volts, whereas the alternator at high speed may well be inducing in excess of 200 volts at high engine speeds - a much bigger test of the insulation of the windings. Therefore there is the real possibility that a multimeter will say everything is OK, but in use it may well not be.
Also, a visual inspection of the alternator windings may reveal some discolouration/burning that may be indicative of them starting to break down. However, that does require the alternator to be removed.
Real time charging system monitoring.
If you're concerned about the state of your charging system and want to monitor it without the faff of getting a multimeter out every time, there's nothing to stop you fitting a small voltmeter. I have a Lascar EMV1200 fitted to the Big Red Bus - my VFR.
Hope that's of some use to someone.