I Grounded the nuetral saftey. They are the same correct?

 

http://3.0spirit.tripod.com/5speed.html
I used this as my guide for doing my swap. IIRC, yes it's just the neutral safety that needs to be grounded, check to ensure you grabbed the correct wire for ground.
Is it possible the ECU you got was bad?

 

That's the same one I used. I currently drive a 92 5 speed. I'll switch them around to make sure they work.

 

What year is your car and what year was the donor?

 

Donor car was 93. My car 91. I just looked up the ecu on factorychryslerparts.com and I looks like they used the same ecm for manual and autos this year. Could this be right?

http://www.factorychryslerparts.com/products/SINGLE-BOARD-ENG-CONTROL--Aft-4-6-91--Aft-5-1-91--From-12-10-90-to-5-1-91--22-Eng-TBI--Man-Trans-Up-To-12-10-90/4267499/04672530.html

 

IIRC they changed fuel injection from low impedance to high impedance in 92. Meaning a 93 ECU will not run a 91. I know this was true for the V6 cars, not 100% if it was the case on 4cyl cars.

 

That would make sense. I'll do some more research this weekend and try some ecu swapping and see what I get. Otherwise I'll just leave the auto ecu in there until I find an mt ecu.