The problem isn't a misaligned frame, but a tank that has gone out of shape when it is off the bike. I have seen this a few times. It most often happens when the tank us full of gas and off the bike for several days.
Generally it can be forced back into position with all parts intact. I can see how it could be impossible to use the big washers. I would use a smaller one rather than just removing it or grinding off part of the old one.