I don't see a problem with JB Weld or similar epoxy fine tuning. Just clean and lightly scuff the back of the dropout in question and put a small amount it there. When it is still "green" put the wheel in and gently adjust until perfectly aligned and let it finish curing.

I would use the steelstik putty rather than the typical resin. You can mold it into position and it won't run out.