Its the ECU, what year ECU did you put in? If its a 91-94 ecu in a 90' that is your problem. I know this because I have a 92 ECU in my FWD which has a 90' engine, just so I could start the car and move it (not driving it).

I believe there is some sort of rewiring you can do.

2012 - Lancer Ralliart Octane Blue
1991 - Talon Tsi AWD FP HTA 71
1992 - Talon Tsi AWD on hold