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i've heard Diesel fuel will help get the crap out of the tank if you take it off. Are you planning on takeing it off. we used to do this to the old Kawasaki 100's we had and it worked. as far as leaving it on and running it with the stuff in the tank, NO.
I was gonna pull the tank, but they won't put it in the shaker to clean it, and I can't use the sandblaster either. (I'm using the hobby shop on the local USMC base)
there is some stuff that is a coating that you can use to coat the inside with that helps kill rust. also i was thinking why wouldn't POR-15 work. it loves rust and covers the inside with a coating of like epoxy. There is a few more ideas.
If you take the tank off and get a length of chain, you can put it in the tank and shake it around to get the rust particles knocked loose. I wouldn't use POR 15 because it's not designed for use in a gas tank. I'd look into The Eastwood Company. They have chemicals that you can use to keep the rust away.