Rear end location wrong? IM STUMPED!!!

All true and good advice. I ended up with the same problem after replacing an entire quarter panel, but only had about a 3/8 difference. Try taking a close look at your 1/16 side to see if it's been replaced or patched. If I ever do that again, I'll fit the new quarter with the new wheel/tire on. Also, the width of the lip on a repop can be wider than OE. If your thrust angle is OK, I would just cut a little bit off the 1/16 side to get better sidewall clearance. Nobody can see both sides at once.
The clearances on both sides were the same before I changed the leaf springs.