Mine was the same way, in fact during a pretty good crash the entire right hand side peeled off in one piece.
I uesd a local auto body paint supply store and had them match the color, that turned out to be very very close to the Yamaha r1 blue.
Painted the bike with proper automotive techniques after sanding all the old blue paint and primer off. Bike still looks great after 2 years and many dismounts. I don't see a need to line the tanks, that can cause a whole different issue.