The gearbox should fit.
With the ecu as it is a auto it will have the stability control so the ecu may spit up some errors as you wont be connecting these up. The ABS computer also is linked to the ecu but I don't know exactly what it does. Supposedly the speedo signal is taken from the abs wheel sensors so maybe this is partly why it is linked. That said I have read of people using the auto ecu and have got the motor running.
You wont be able to use the 2nd gen ecu as the 4th gen ecu has coil on plug, crank angle sensor and different tune (compression is higher in the 4th gen 3sgte)
Ecu pinout
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