Howdy,
I have a 06 GT (stock except for wheels and tires but not for long…). I agree that the brakes could feel better, and though I have yet to open track my car, I would suggest high-performance pads and stainless lines before going with an potentially unecessary and expensive brake disc and caliper upgrade.
Prior to my GT, I had a very highly modified 1991 Taurus SHO with 11.6in discs, dual piston PBR calipers (same as those they used to use on Vettes), Performance Friction Carbon-metallic Z pads, and stainless steel lines. This set up was up to the challenge of open track. I wouldn't try an enduro race on such a set up, but it was VERY cost effective and actually performed quite well.
Surprisingly, the SHO and my 06 GT weigh about the same. The GT has 12in+ rotors stock, and calipers that are actually stiffer than those that I upgraded to on my SHO. The stock discs plus some high performance pads and lines will work wonders, I promise. At least try this before laying out really, really big cash on a full break upgrade. If you want to step it up a notch, you could add a proportioning valve so that you could dial some additional brake bias to the rear, allowing that all four tires are doing their part in stopping the car. Although the stock discs are not slotted, you can achieve cooling effects with some ducting and a little work to direct air at the center of the discs.
You should be able to find pads and lines for at most $300.