The difference is just the manner in which the clutch is actuated. Each has it's pros and cons. The easiest way is the cable setup since that's what the car was equipped with originally.
The rear end is fine and really isn't effected by a
trans swap.
Unless you know someone who owns a shop or have family that owns a shop, take a jar of vaseline with you. It'll ease the pain. Most shops won't touch a job like that especially if you drop a load of used parts at their feet. The shops that will touch it are custom shops and "custom" is apparently Latin for "effin' expensive"
Here's the deal. If you can't change a tire, do a tune up or change oil, sell the car, and buy one with a 5spd or live with the automatic. If you really have no clue, "but wan't to learn" I don't think this is a learner's project especially if the car is your daily driver. It's not difficult if you have a clue. I did the job over two days with no more than 6-8 hours on both days. I did the pedals first, and then the following Saturday swapped the
trans. But I've been doing crap like this since the early 80's
The only true performance automatic option for the 2.3 is a C4. The downside is that it's not an overdrive automatic. There's an adapter plate being made now that adapts Windsor bellhousings to the 2.3 block. This opens the door to a couple more options on both the automatic and the manual side. 6spd anyone?
Search teh interweb for stinger performance. There's a how to article on 5spd swaps there that's pretty good. There's a few details missing, but nothing that hasn't been covered in this thread.