Toyota Repair: ECU, service transmission, barking up the wrong tree

Question
I have a 1996 Rav4 that I bought cheap. I,m trying to diagnose a "jerky" running problem when doing over 45mph. The fuel pump output is a steady 52lbs. The plugs, wires, cap and igniter are all new as well as the fuel filter. The engine light is always on, and the OBD shows low EGR vaccuum with a service transmission message. Could this be caused by a 2 wheel drive ECU in a 4 wheel drive vehicle, or am I barking up the wrong tree? The ECU number is 89661-42140 and it looks like it came from a junk yard...Thanks

Answer
Since the check engine light is always on the first step is for you to let me know what the diagnostic trouble codes in the computer are, I need the code numbers, verbal descriptions mean very little to me, after I have the DTC numbers I may be able to help.