8350 on GA-990FXA slow networking

Sounds like something is wrong with the hardware then. If something is wrong with the PCIe bus it should be very noticeable in graphics benchmarks and such. I least I would think so, not sure how to reliably test it, maybe AIDA64 has something there (non free software though).

I would try to eliminate as many fault-sources as possible, try connect the machine directly to the NAS with a cable I know works with another computer etc.