Basically the N/A ECU also houses the transmission computer (that's why the transmission works)
The Turbo ECU doesn't contain the transmission computer, so the transmission shits itself and goes into limp mode (2nd gear)
If the guys are awesome they can piggy back the turbo ECU in parallel with the N/A ECU and it'll work just fine. Basically have two ECU's but cut the wires that drive the injectors and ignition packs coming from from the N/A ECU plug. This allows both ECU's to see all of the correct signals, but allows the turbo ECU to do the work controlling the engine, and the N/A ECU left controlling the gearbox.
Realistically there are only the key wires that need to stay connected to the N/A ECU.....Pins # 4,5 20, 24, 25, 29, 31-41, 44-46, 48, 54, 55, 58, 60, 67, 70, 72, 79, 80, 113, 115, 120-122
Maybe a couple more, but that should be it