When I built my system, I used the 3rd party USB and and extend port limits options in Clover. Through Apple's System Information utility, all USB 3 and USB 2 ports report at their proper speeds (either 5/Gb/s or 480Mb/s, respectively). Two USB C (also used for Thunderbolt 3) don't show up or work as USB, but I'm not sure it that's a configuration setting or due to the fact that I don't have a proper USB C device (I've bee trying a USB C to USB 3 adapter, but all it seems to do is apply power the whatever it's hooked to).
Sometimes I do have to reboot the machine to get a USB 3 device to show up when I move it from one port to another.
I still have a lot of testing to do with respect to USB speeds and Thunderbolt, but at least the devices are visible.