I had the same problem when I bought my 2001. I worked on ships my entire life, where rust is a constant problem. We use a product called Phosphoric acid to neutralize rust as it chemically changes iron oxide into iron phosphate, which acts as a barrier to further oxidation. Here is the post I wrote up last fall.
I assume you have the tank off the bike, if so set up a table with a soft blanket, drain most of the gas into a container and set aside as you will use it. Place the tank upside down on the table. Use a pair of rubber gloves and a coarse 3M pad and reach inside the tank and scrub everywhere you can reach using the old gas as a solvent. This sound tedious, but does not really take that long. When done, prop the tank upright, I used some line to hold it up and use a hand pump to remove the gas and rust into a shallow pan, like you would use for an oil change, and set that outside in the sun. The gas will eventually evaporate leaving the rust and a bit of sludge which can be more easily disposed of rather than all that liquid.
Repeat this process using your old gas until you feel you have gotten everything you can reach out of the tank. Let the inside of the tank dry for a day or 2. When completely dry, take about 1/3 of a litre of fresh gas and use a fresh 3M pad and scrub the inside of the tank again. If the gas turns brown or rusty, drain and repeat until scrubbing with fresh gas does not discolor it. Drain and let the tank fully dry again for a few days or so.
Remove your fuel pump from the plate it is attached to while waiting for the tank to dry, you will need it to plug the hole when you add the Phosphoric acid to the tank. When the tank is dry, add about 1/3 of a litre of the acid, and with rubber gloves and a fresh 3 M pad, srcub the inside of the tank. If the acid turns brown from rust, drain and repeat until its fairly clear. I let the tank dry for a day, but at that point you can add about 1/2 litre of acid, seal the tank with the plate, plug the fuel lines and turn the tank around 360 degrees in each direction. When fully coated remove the plate and drain the acid into a container and save. Let the tank dry completely and inspect, it should look pretty good by now. If it does, take the acid you saved and put into the tank and repeat this last process one more time, then drain and let the tank dry. If all goes well it should look like mine in the post.
Note, I do not live in a very warm place, if you happen to this process will go much faster. It took me almost 4 weeks, but 95% of that was waiting for the tank to dry.
Note. Phosphoric acid sound like a strong thing to use, but look at a can of Coke, its listed as one of the ingredients, so if you can drink something that contains it, well, its not so bad,
Note. Phosphoric acid will discolor paint if left on a surface , so be careful when pouring and removing. I keep a spray bottle of water handy along with some rags to clean it up if it does happen to get on the paint.
Note. Letting the old gas and rust evaporate in the sun means you do not have to find a way to dispose of it, same applies to any left over old acid.
Note. If your pump still functions, you can carefully clean it also with the acid. I used small acid brushes and Qtips. Do not soak the entire pump in it. if the tank is that bad you probably should replace the pre filter and primary filter for peace of mind.
Note. When done, I do not recommend you coat the tank with anything. A look inside the tank should be explanation enough for why this is not a good idea.
Note. Do not use any Phosphoric acid product that is not a thin liquid. There are some out there that are Gels, avoid those as they will leave a residue in the tank that will ruin an otherwise great day on your bike.
Hope all of this long winded post proves to be of some value to you. Take heart, you can get through this and be out riding this summer, it will just take some time and elbow grease.
Best of Luck, and don't hesitate to PM me if you need any clarification to what I posted above.
Regards, Michael
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