Pathfinder auto transmission swap

I have just had the local Nissan dealer put a used transmission in my 90 Pathfinder as the old one only had 1st gear. The new transmission is out of an 89. Now they advise me that the new transmission only has 3rd gear. They figure that the computer is shot and the vehicle is in "limp mode". I spoke to the wrecker who sold me the transmission and he stated that he personally tested the vehicle that the tranny came from and it was perfect. He loaned me the computer for the tranny and I tried it in the vehicle but it was not compatible with the rest of the wiring. So...I don't know if I should buy a used computer and try it or go back to the dealer to get them to confirm that the rewiring they completed was correct. Any suggestions?