1. Having a computer like a MicroTech, I'm guessing it would most likely cause transmission issues not too far down the line. The factory ECU has some sort of an ignition cut-out to ease pressure on the gearbox during changes, and I seriously doubt the MicroTech would have this function in it. If you were to get a better computer (like a Haltech, MoTec or similar), then it *might* have functionality for the ignition cut during gear changes.
My car is an s1 with an R34 GTt PowerFC, but the guy I bought the car off had already converted it to manual, so when I had the PFC installed about a year ago I didn't have these issues.
2. Converting to RWD is pretty easy, and as long as it's done right, you shouldn't have an issue. BUT, you'd barely save any weight - removing the driveshaft from the transfer case to the front diff will save you less than 10kg. The Nissan ATTESA system is a constantly variable system anyway, so for maybe 80-90% of the time the car is already in RWD mode.
3. Standard front brakes are twin-piston fronts and single-piston rears. A good-quality brake fluid, and as already mentioned, a good set of pads, will work wonders. Braided brake lines would also help (but make sure you get some that are ADR-compliant).
Being a 96 model, it would definitely be an S1...
The ECU shouldn't have a problem with the front driveshaft being removed, but yanking the diff out would most likely involve removing the engine (IIRC, the diff is attached to the bottom of the block) and changing your sump for a RWD one.
Nope, R33 GTSt/R32 GT-R brakes are NOT a direct swap. There are plenty of threads on this, have a good read through and all will be revealed...