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:
"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"
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:
This is working on Ubuntu 16.04.2, Kernel: x86_64 Linux 4.4.0-66-generic