[lt1_fd3s]

To help answer the initial question of trans swap: I've done three of them, once for myself and then for 2 friends.

You do not have to swap out the ECU nor do you need to swap out the emissions harness that runs from the ECU all over the engine. You will have a handful of plugs from the transmission you will have to zip tie up out of the way.

also, there is a little box near the ECU (I believe it is a little black electronics box) that can be removed. My car would backfire upon shut off until I removed it. I've not done the swap in a few years so I can't remember exactly what the box is called.

as for the driveshafts: the flanges that bolt the driveshafts to the diffs are different. the auto has a larger bolt pattern than the manual. also, the length of the driveshafts are different. I believe the manual shaft is about 1'' to 2'' shorter due to differences in the diffs themselves. I've been told you can take your diff apart and swap out the "input shaft" on the diff to deal with the length and the bolt pattern. I personally purchased a manual shaft and then swapped out the u-joint and flange on my auto shaft to the manual flange. my brother was able to pull off this feat, but a drive shaft shop may be able to do it for you.

good luck.