88 transmission problem

I have a 1994 Olds 88 and I had a bone yard transmission put in by a shop and now the transmission shifts out of first perfect but it won't shift again but the car accelearates and the car was placed on a machine with a trusted transmission shop and the machine showed that the computer is telling the transmission to shift but it's not, but some time it will shift again at 50 mph and when you put the floor shifter in 2 it shows up on the dash as 1 even when its in 2 could a bad wire harness cause this problem or the linkage to the gear shift. I forgot it has a 3800 motor.