The R154 uses a different flywheel, clutch assembly (obviously) and driveshaft...and, obviously the bell housing is different. Make sure you get all the right parts if you're swapping one in... it'd suck to get everything apart and realize your car's going to be sitting in the garage for a week now while you wait for a bell housing.
I don't know about swapping auto for manual in the MKII; If it's anything like the MKIII it's not involved at all on the electrical side, but I'll let someone who knows the specifics cover it.
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