exhaust, shifter, throttle-bodies

The general consensus is that straight through style mufflers will free up more power when comparing them to chambered style mufflers. As long as you are ditching the factory sized 2 1/4 diameter exhaust plumbing, you are on the right path. Replacing the factory midpipe (whether it be an X pipe or an H pipe) and catback should yield some pretty solid gains. If you can splurge for headers as well, even better.

Exhaust preference is such a subjective matter though; be sure to pick whatever your ears like best - listen to a few different exhaust combos in person before you decide.

I think you're probably splitting hairs about the shifter as well ( ) but you can't go wrong with either brand you mentioned - good reviews from owners of both brands (Steeda and MGW) are plentiful on the message boards.

Your thoughts regarding aftermarket throttle bodies on a stock/bolt on car are pretty spot on - it's not going to free up that much power. Consider other mods instead ( ie - gears, pullies, or just go forced induction ).