Just be careful -- I bought a used MSI motherboard with an Opteron CPU and 2 PCI-E slots, but they didn't work with most modern video cards! Turned out they were PCI-E 1.1 instead of 2.0, and this particular mobo had problems with certain video cards -- such as ATI 5XXX and 6XXX series cards, that's all...
It must be something other than PCIe 1.1 that was causing issues. PCIe is both forward and backwards compatible.
PCIe 1.1 card in 2.0 slot is fine.
PCIe 2.0 card in 1.1 slot is fine.
You are simply limited to bandwidth of the lesser protocol but then again a serial cable has more than enough bandwidth for a miner.