New PC

[CAT-THE-FIFTH]

So, the opinion seems to be that if I just upgrade the GPU, I shouldn't see any noticeable issues running a PCI-E 3 based card on PCI-E 2?

I was running an overclocked HD5850 1GB on a half speed(8X) PCI-E 1.0 times slot for years,and by that time PCI-E 2.0 16X was common.

For single card setups you should be fine IMHO.

Plus,you can always upgrade later on if the CPU or platform becomes a limitation.

However,also like I said ex-server six core Core i7s are cheap now,so there is still much life in socket 1366 IMHO.

[Bonebreaker777]

My motherboard doesn't fully support PCI-E (I think) so wont that cause a bottleneck? :/

You mean don't support version 2 or version 3. As long as you have a PCIe slot, it is supported.
And the differences between versions (version 1.0 vs 2.0 and/or 3.0) is only a couple of percentage so you are all right.