rear end off

The driver side measure 5 9/16 from perch to hub surface, the passenger side is 9 3/4" from same point. All I know is there was probably 1" to 1 1/16" of clearance between the wheel and fender on the drivers side and about 3/8" on the passenger side.

Uh, 5-9/16" vs 9-3/4"???

Those numbers should be the same. Not even the factory screwed them up that bad, you're talking about a difference of over 4" unless that's a typo. For an A-body 8 3/4 with SBP axles the measurement should be 5-13/16" with from the outside of the perch to the wheel mounting surface, assuming it was dead on the factory specs. If your measurements are really that far off not only are the perches not even close to centered, but that's not even an A-body 8 3/4.