Where did the loom come from, did it have an ecu with it etc? If it is from an Aussie car, did you get the key, ignition, transponder ECM etc?

I would say your confusion may stem from the early models. A V2 STI ecu can be put into an RS lib and is a good step up. Later models are not as compatible.
The wires that need swapping are in a few threads here, do a search for power fc install and you'll find it. I think it is cam and crank angle sensor wires that are switched.