You are nuts to take on that job all at once - espcecially when you can't see the wires! This is what you should do:
1) Finish the AWD conversion and install the 5MT. Presumably this is the RS tranny (why you have a clutch slave cylinder installed I have no idea). You are more than half way there already. It's like a weekend of work
2) Get 16" wheels and put in RS brakes on the front. They are always selling OEM wheels here for a few hundred.
3) Giver. This will be a fun setup for cheap.
4) Make a decision later about the conversion once you have exerience. It's a BIG BIG job that will cost $$$ or will never work properly.
You don't need a new ECU. I have done this and in fact have a 2.5 DOHC running an STI tranny on a 1.8 auto ECU... and I just rallied it at Oregon Trail!
PS I'd buy that motor and link if the price was right.... let me know.