You're right, I used the wrong version of NVFLASH. I just successfully flashed my EVGA GTX680 SC card, and it is indeed using PCIe ver. 2.0 in OSX as well as Bootcamp Windows 7
Lost a few MHz on the GPU Clock (1059->1006MHz) and the Memory (1552MHz->1502MHz). This of course results in a slightly slower Pixel Fillrate (33.9GPixel/s->32.2GPixel/s), as well as a slower Texture Fillrate (135.6GTexel/s->128.8GTexel/s).
Now onto overclocking the card to it's former glory
Thanks to all for your help and guidance!