There's a separate TCC (transmisison control computer) that takes temperature, speed and throttle position signals from the ECU (and transfer case range, but I imagine that's a direct feed from the transfer. You can patch an auto TCC onto a manual computer an get it to work.
Probably easier to find an auto donor car if you are looking to swap to an AW-4 auto though.
Yes, the loom can be stripped heavily. You really only need the engine loom, which once you get the whole loom out the the car, you will see isn't very big. Then it's just a matter of locating and running the VSS and check engine light wires.
As an example:
2000 Baleno loom:
Just the engine loom:
Except for one wire incorrectly connected, I had this stripped, shortened, and in the car without a diagram and without error.
It's not hard, just time consuming.
This is the shortening process:
before shortening:
After shortening:
And the finished engine bay:
EFI engine bays don't have to look messy.
Steve.