First thing I would say is you need to stop using the generic PXSX to XHC rename patch as it is catching a number of other devices that shouldn't be renamed as XHC, including the FireWire, Ethernet and one of the SATA controllers
View attachment 543578 Section of IOReg with PXSX renamed devices.
I think you may need to use something along the lines of the renames below, so as to have just the Usb controllers renamed to XHC2 and XHC3.
Rename: RP05/PXSX to RP05/XHC2 - Find 525030352f50585358 - Replace 525030352f58484332
Rename: RP06/PXSX to RP06/XHC3 - Find 525030362f50585358 - Replace 525030362f58484333
Being more specific with the rename patches should prevent the Firewire, Ethernet and SATA controllers being renamed to XHC along with the Usb controllers.
Second thing is all the USB ports under the two XHC USB3 controllers should be set with the connector type 0x3 (USB3) even the virtual USB2 ports. As it is the physical ports characteristics that need to be used.
All 8 x ports should be set as 0x3 (USB3).
You have the 4 x USB2 virtual ports set as 0x0, which equates to USB2 connector type. This is wrong.
The screenshots below show the configuration of the 4 x USB ports under the /_SB/PCI0/RP05/XHC controller.
View attachment 543585 View attachment 543580 USB2 virtual ports
View attachment 543581 View attachment 543582 USB3 physical ports
As can be seen the first two screenshots show the ports are set as 0x0 (USB2) and the second pair as 0x3 (USB3).
This is the same for the 2nd XHC USB controller.
Regarding the EH0x USB controllers:
View attachment 543586 EH0x controller ports
There are 6 x USB2 ports under the EH01 controller HP12 , HP17, HP18, PRT1, PRT3 and PRT8. The numbering/ordering of the ports is quite strange. I would expect HP11 through to HP18 or similar, not the disparate numbering/ordering that is present.
The 6 x USB2 ports under EH02 are more what I would expect to see. Port numbers HP21 to HP26 inclusive.
Of the 12 x Usb2 ports shown, only PRT8 doesn't use the USB2 0x0 connector type. PRT8 has 0x2, which I don't recognise. This may be a USB port connected to an Express Card?
Your IOReg shows no ports set as internal, i.e. from a USB header port, which should be set as connector type 255 (0xFF), even though we know some of these USB2 ports are served from an Internal USB2 header.
Which of the 12 USB2 ports are shown as active the IOReg when you insert a USB2 pen drive or other USB2 device?
Can you test this and make a copy of the IOReg, when you have tested all the external USB2 ports. Post a screenshot of the two EH0x controllers, if the details from the testing doesn't carry over to the IOReg when you make a copy.