Well I’ve gone through and tested several different versions of BIOS, and I even completely replaced the motherboard with a brand new one. Yet, I’m still able to use the USB ports, and I have only been able to re-create the problem that
@kgp pointed out about missing the entire XHCI ACPI table in my I/O registry when disabling 4g encoding in the bios.
So, the USB ports are back, but I still have the Finder crash occasionally when I unmount a drive. I get a Beachball that never stops, and, if I read launch the Finder, it clears the desktop but it never loads back on and I have to reset.
The other major issue that I am having is that my Qtake software which had been recording video with the black magic 8K card, is no longer able to record the video, and I get corrupt files. Everything was OK for the most part with this machine outside of the USB issues until I attempted to install the Alpine Ridge card. Other than installing Windows on a separate drive and trying to install the Alpine Ridge card in slot 5, (which I removed after I quickly learned it will not work it has to be a slot two) I really didn’t add anything except for the SSDT-C299-TB3HP which I have since removed. I have also turned off the Thunderbolt support in the BIOS. To be clear, I have abandoned the Alpine Ridge card in this system for now so it’s no longer part of the mix.
I did extensive testing today including testing the card in a Thunderbolt three enclosure on my iMac, it works fine there. I tested various different versions of the software, which is anyway usually very reliable,. I tested the media express app from black magic, and it is able to record just fine. I also tried a different version of the driver for the card just to reload the firmware, and then went back to the driver version that I’m supposed to use. Once again reloaded the firmware for that. I just can’t figure out why I can’t get back to where I was before and I started that Alpine Ridge install.