I have a 1992 Camaro with 4 wheel disc brakes. When I go to stop the stopping is jerky but no pedal pulsation. Car stops straight and has a firm pedal. The stopping is the same if I put the car in neutral. I feels more like it is in the rear than than the front.

I have done the following work on the car:
Rebuilt master cylinder
New disc pads all the way around
Turned all 4 rotors
Rebuilt caliper assemblies all the way around
New front brake hoses
Bled the system properly

The previous owner changed the rear gears from 3.23 to 3.73 and apparently did not get them set up right since they are noisy. The computer was never reprogramed for the gear change. Could this be the problem?