Ok so for anyone with "GIGABYTE GA-970A-DS3" I have done alot of testing and research. The best config I found to get USB3 working is this:
Edit Grub config:
sudo nano /etc/default/grub
Edit the line that looks like this:
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"
Add "amd_iommu=on iommu=pt"
to the end of it so now the line now looks like this:
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash amd_iommu=on iommu=pt"
Update grub:
sudo update-grub
once you have done that reboot the system and hit DEL / Delete key to enter BIOS/EUFI setup:
Ensure IOMMU is enabled, XHCI handoff is enabled, EHCI handoff is disabled, USB Legacy support is enabled. OS type I have set to Windows8 but I have CSM enabled "Compatibility Support Module" so Linux will boot via BIOS emulation instead of UEFI.
This fix allowed my USB3 to work properly and fixed a few audio issues.
For bonus fix if your running a x64 bit Ubuntu and find USB transfers hang at the end apply this fix:
https://gist.github.com/2E0PGS/f63544f8abe69acc5caaa54f56efe52f
This is working on Ubuntu 16.04.2, Kernel: x86_64 Linux 4.4.0-66-generic
Thank you so much, I've spent several hours trying so many alternatives. My PCI network card would not work on this board (as well as the USB problems) but your fix has solved the problem. I was about to send the board back believing it must be faulty.