Engine Computers in Auto/Manual

Hi guys, I'm new to the forum but have been lurking since I bought my wave. The only issue I have with this car is that the suspension is soft (H&R springs soon) and it's SLOW. I had a 2.0 golf before (the slow one) and it was just a bit faster.

Anyhow, I've read all over that the 1.8 is a drop in replacement for the 1.6. But I would like to know if pulling a motor from an auto car (most of them in wrecking yards) would pose an issue when I put it in my manual car, or if I can just take my transmission and wiring harness and pop it in.

In a more extreme scenario, if I pull a 1.4T from an auto cruze WITH the ECM, will the ECM know it's missing the original transmission? Or is it 2 separate computers for engine/trans

Thanks in advance :)

Just buy a fast car.