Being really curious now about my bike, I looked again at the clearance between the washers and my tank at the mounting slots. Very little clearance between them (maybe .020"), but just enough to allow maneuvering of the tank and installation of the mount bolts. Seeing how much you've had to grind from your washers maybe there was indeed some misalignment at the factory when everything was first fitted up.
Looks like you're back in business and glad you were able to fix the breather pipe.
Current: 2014 R1200GSW & 2007 DR650