Gtx 680 build pci 3.0 on 2.0 Mobo

Your processor will perform noticeably less than your graphics card if you decide to go with the GTX 680, I would suggest going with an Intel CPU unless you are already committed to the AMD CPU or at least go with the FX-4170. You could also go with a GTX 580 which would be more on par with your CPU and bypass the whole PCIe 2.0/3.0 issue, although the performance difference between 2.0 and 3.0 is only evident in extreme systems in games with extreme demands, not the majority of games. Going this route would also allow you to save some money in other areas of your build, the 16GB of RAM can be scaled down to 8GB (2x4GB) and getting a lesser power supply (500-600W). You could use this extra money to justify the jump in processor and maybe get a Solid State Drive that would make your system much more responsive and decrease load times.

Hope that makes sense to you. See this for Graphics Cards and this for CPUs.

PCIe 3.0 is backwards compatible with PCIe 2.0. You won't see the difference.

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Get an Inetl CPU or wait for PD. And why the 680? The 670 performs so close to the 680, that paying the $100 premium for the 680 is not a good choice.