Help us help you. By posting the year, make, model and engine near the beginning of your help request, followed by the symptoms (no start, high idle, misfire etc.) Along with any prevalent Diagnostic Trouble Codes, aka DTCs, other forum members will be able to help you get to a solution more quickly and easily!
Transmission? Without having a diagram handy I'm not sure.
I don't want to discourage you, but I think it would be a great effort to take the harness wire for wire and try to put them in their respective place to the other computers connectors only to find that it probably won't work.
If you do get it to work let us know!
I think there's guys who piggy back modules into the old Ford EECIV modules to run newer automatic transmissions in Fox Body Mustangs...
You have saved me months of hard work for nothing.
Transmission is completely mechanic (no solenoids inside), so with this information about that green connector, i suppose pcm is going to through out DTC's and give some problems.
Also about injectors, that would be a long work. I mean, change intake manifold and get injectors and stuff.