I'm not sure if this is universal across the board for wheel well arches or not, but I had a wheel well arch replaced twice on a Maxima I had that I bought with some minor cancer on the lip and both times it ended up coming back through...I went back to the guy that did the work the 2nd time and...
I'd recommend Pypes Exhaust for everything but the actual mufflers, I had a set of Pypes mufflers and they made the car sound a tad ratty to me. I have been very happy with the Pypes x pipe I run, plus it is priced pretty well.
Hard to say, you did not mention whether or not the exhaust is completely stock at this point or not. A typical metric/standard mix of sockets with a 3/8" ratchet, mix of wrenches, and a few extensions should serve you well though I'd say.
There is no way I'd waste my time with a 4 lug brake upgrade personally. There is even less of a chance that I would ever spend $3500 on a set of wheels for any vehicle, let alone a fox mustang that is barely worth $3500 with that set of wheels on the car!