As per improving the GT there are not very many areas that need/can be improved.
- Engine: this is the component that has seen the most options avaliable. You can go from a simple pulley swap ($600 and add 60-70hp) to a Twin Turbo set up ($35k and 1,000hp) going through a Supercharger swap (for a Whipple => $10k and 720-730HP). The choice is yours depending on how you want to use the car.
- Transmission: the Ricardo 6-speed gearbox was developed for the GT and it's an incredible piece of engineering. The only possible mod would be changing the diff ratio.
- Suspensions: the GT stock suspensions are really woderful. To better them you really need to vent into the competition range. Penske and AT (right guys?) offer packages of double and triple adj shocks/coilovers. The ride get a little firmier and you can lower the car (careful with the aerodynamic consequences) a little. The improvements will be evident if you track your car. The car has a tendence to understeer in corner entry. The upg suspension will allow you to sharpen up the turn in and dial out the understeer completely.
- Exhaust systems: there are a number of mufflers avaliable. Check the Tech session. At the top there is a sticky with a compilation of the muffler sounds. You can change the muffler only or go all the way and replace the headers.
- Exterior: there is little avaliable because the car is just perfect. But you can get a X1 treatment (avaliable until Aug 08), swap the front splitter and rear diffuser with more aggressive ones (Stillen), get a Guerney bubble if you are a tall driver and track the car.
- Wheels: there are a handful of options readily avaliable (I-forged). Then there is the custom race-wheel build route (CCW, Jongbloed, BBS, Fikse, Kodiak etc) and then there is the retro option in the making (for more info look up for Kirby's msg about the Halibrand GT40 wheels).
- Brakes: the stock Brembo are fine unless you extensively track your car. Swap the pads and change the fluid. There are talks of ceramic rotors being in development (they will possibly need a change of calipers too) and there are 6-piston caliper kits avaliable for the racers (Stillen)
- Interior: Kip Ewing has developed a nice carbon fiber catalog to choose from. Items include the ceter console, Mac sub enclosures, storage bins etc.
All in all Ford really did a wonderful job with the car at launch and the possible improvements are finite and debatable.
I think of the 6 options (color, Mac, wheels, calipers, stripes, year) that you have the most improtant is the color.
They all look great. I have had the chance of seeing a lot of them next to each other and I would be happy to drive home in any without any regrets.
The Mac is the most common options and it will be extremely rare to find a car without it.
Second most common option are the stripes. A car without stripes is considered very rare.
So after the color (Mac and stripes are given) I would not be too hung on the year, caliper or wheels.
Find the best car from a reputable source. The savings that can be had by venturing in the unkown are not worth it.
Good luck in your search. You are in for a treat. You won't be disappointed.