PCI Express 2 and 3 are compatable with each other. It will just default to the speed of the PCIX slot or the GPU, whichever is slowest.
But, current Gen3 Graphics cards can not even saturate the bandwidth of a PCI 2 slot, so there really will not be any difference in performance.
I would just grab the best GPU you can afford and go with it regardless if its a PCI 2 or 3, or which board you choose. At this point in time it makes no performance difference. Likely, the next generation of GPUs will not either. But after that, it very well may.
In regards to the CPU, just be careful and be aware that switching the motherboards will require a clean install of Windows, to prevent any conflicts or issues.
What board is the new one?