I have the identical problem to the OP, JoeStldes. Same GA-990FXA-UD3 motherboard except Rev 4. Running Ubuntu 13.10 and I've done nearly the same steps in troubleshooting. Currently using (trying) the r8168 driver.

I just now enabled IOMMU in the BIOS and it prevented any USB ports from working, thus no keyboard or mouse. No network difference it seemed.
JoeStldes, have you tried enabling IOMMU and has it worked?

Resistent, when you enabled IOMMU was there anything else that you had done to get that to help you? Any ideas why my case is the opposite result?

Couple more days and I'm going to buy an Intel NIC and use the functioning internet connection to research ways of coping with failure...