I know this is REALLY late to the party, but I have been using the GA-970-D3P sine Ubuntu 14.04. I now run Ubuntu 16.04. Each distro runs great.
First off, you need to disable IOMMU in the BIOS.
Second, you need up update your GRUB.
sudo nano /etc/default/grub
edit the GRUB_CMDLINE_LINUX="" to read GRUB_CMDLINE_LINUX="iommu=soft"
Save and exit nano.
Update grub with sudo update-grub.
Now reboot the machine, your USB2 and USB3 ports will work just fine. All other hardware with this motherboard works OOB.