Hello RehabMan,
After much wrap your head so that the USB 3.0 ports on my PC worked, I descobriri something that may be crucial to resolve the issue.
My system is dual boot: Windows 10 and os x Elcapitan.
I booted the windows with the HD connected and tested the USB 3.0 port and was worked perfectly. Reniciei and went to the El Capitan and to my surprise all my devices were connected to USB 3.0 that was not connecting any devices. I installed the FakePCIID and FakePCIID_XHCIMux Kexts to see what was happening. Recializei and there were all the doors working both USB 2.0 and USB 3.0.
In short: The USB 3.0 ports only work if first I inicializr windows and renicializr o x Capitan. It is to solve this problem so that the USB 3.0 ports will function without having to go through the windows?
I thank you for the dedication you have to help us in situations as difficult as this.
A big hug and be with God.