I have a 9010 MT (MiniTower). I installed Mojave without the front usb header connected. After installation, the rear ports including the SS (superspeed) USB 3.0 were working. I then connected the front usb header, and now only the USB 2.0 ports front and rear work. The SS (superspeed) USB 3.0 ports do not detect devices at all. I assume it's an issue with port limitation and that the SSDT provided so nicely with this guide is for the SFF (slim form factor) which has a different assortments of USB ports.
When I was running Sierra on this Optiplex, I just used a PCIE USB 3.0 card, so some advice on where to start to troubleshoot this issue would be super. I started down Rehabman's guide of creating a custom SSDT for this machine, but considering I can't even get the computer to detect on the SS USB 3.0 ports, I don't know where that port is in the device tree.
Additionally, if you'd like to see pictures of how I got the front usb header plugged in, access to all 4 sata ports, 2 sata SSDs, ODD, and a 3.5" drive along with a full size 7950, I'd be happy to post those.