Dennis--The issue I noted of the muffler warping the case (and liner) wasn't from misalignment of the bolts. Rather, the muffler interface surface was sandblasted, not machined, and it wasn't flat. Pulling a non-flat muffler up against a machined-flat engine case warped the case and caused binding as the engine warmed up.
C.T. and Lauri--Ok, I understand your comment on axial clearance over operating temps. I haven't seen one that tight before. If I already had the engine apart, I'd lap the nose of the case so that messing with washers wouldn't be needed.