Just going on a hunch here, but I think you may be using a Speedway Motors kit with the 5 1/2" bolt circle rotors. Those rotors are shown as 1.200 nominal thickness and the GM calipers you are using are for a rotor with a thickness of 1.050. I wonder if the extra rotor thickness is just great enough for interference even if the caliper pistons are retracted completely; when the anti-squeal pads were removed it may have helped the clearance issue. Could you mic your rotors for curiosities sake?