Try just unhooking the speed sensor from the transmission. That will tell you if it is being caused by the speed signal or if something else is going on.
The stock ECU would have used the speed signal for controlling the automatic. I think should work fine without a speed input.
My documentation doesn't have a pinout for your ECU, but if you determine that the speed signal to the ECU is you problem, you should be able to trace the wire from the sending unit and figure it out from there.
