I have a 1997 Trans Am. I broke the rear end and got one from a 1994 Camaro that was an auto, I am a six speed.
Every since I put the rear end in, the caliper's on both sides are rubbing the rotors.
It rubs on the inside of the rotor. Almost as if the rotor was too far towards the center of the car. The bolts that hold the caliper in, Which come from the middle of the car to the outside, were also rubbing the rotor.
Any suggestions why? It acts like the axles are too short, or something is set up wrong
Any ideas?

 

Same thing happened to me.... broke my 95Z rear and bought an "Umbrella style parking brake" rear. It's same as mine, but don't know the year. It also rubbed the caliper as you mention. I just made a 1/16" spacer to place under the rotor and prevents any rubbing. Did your replacement rear come with this "strap" style parking brake system?

 

it could be possible that the rear you have is setup for the LS1 brakes.

LS1 axles are just SLIGHTLY shorter, and if you run LT1 brakes on a LS1 axle, they rub the caliper "carrier"