I would go with a 3" section of pipe and put in a new resonator at that point. What is probably on the car is the dynomax piping - It is 2.5" and pretty nice quality considering the price. However, it will choke off the car up top. I would definitely keep the resonator - it does not hinder flow and makes the car sound a *lot* better. Removing it is a great way to see a lot more rasp and noise. I've never heard a SHO that sounded good without a resonator. Does your car have cats?
If you are planning on a TwEECer and a wideband, I would not worry about hitting the dyno again. If you change the exhaust it would be a good idea jsut to make sure it does not lean the car out too much at high rpms, but aside from that its just bragging rights.
Also, consider having them modify your Y-pipe to have a 3" collector to match the 3" piping if you decide to up the size. That will also help flow (and, subsequently, horsepower) considerably.
The gatorback has a lifetime warranty, but it is probably only to the original purchaser, so you may end up buying one more at some point - However, after that, they're all free. You may also want to look into the Reichard Racing pulley like Lupo has (pictures and a link were posted fairly recently), as they should also eliminate belt slippage and help you hold the boost with less wear on your tensioner and accessory bearings from the extremely tight belt.
With the copper autolites, try running on the small end of the factory gap, or even a little smaller (.042" is the factory minimum - maybe around .040" ?). Murph's input is probably more worthwile than mine here.