It sounds like the stiffness that the brake bridge adds to the seat stays kept the upper part of the rear triangle from bending symmetrically for some reason. If you had access to an alignment table, you could measure that, but fixing it might not be that easy. You could use something like the park tools fork alignment gauge to check to see where the brake bridge hole is, I guess they don't have one for the rear triangle though. You could add washers to the fork tool. I think you can use the FAG-2 to do this too. Just check the side to side alignment at the brake bridge. Not quite as easy as the dropouts, but you should be able to get an idea.