Afaik there is very little you can do in Bios to improve GPU performance, running on PCIe 2.0 instead of 3.0 costs you maybe 2-3% so it's no big deal (could not find any data on the 295x2 unfortunately so it is only an assumption based on earlier PCIe 2.0 vs. 3.0 tests).
The review on Futuremark puts the 295x2 at 26k points and you are on 22k-24k for the GPU so it is fine I think. 3DMark11 is a fairly old benchmark so I would not be surprised if there was a small bottleneck in the engine itself regarding CPU utilization. Have you compared 3DMark Fire Strike scores yet?
Btw. there are 2 scheduler patches for Bulldozer/Piledriver CPUs on Windows 7 that help a little bit with poorly threaded apps just in case you haven't installed them already 😄