Just an idea, seeing as the stagea needs the standard ecu to run the auto gearbox, can't you leave the standard computer hooked up to the loom, still receiving inputs from the sensors and sending instructions to the auto, but not let the standard computer tell the injectors, timing etc what to do. Then, get a Power FC and splice it into the loom and away you go.
Might require some fiddling here and there to make sure that the correct voltages are going to the ECU's.
Just throwing the ideas out there.