Okay great.
I don't have your motherboard to test, but we can see clearly from the Hackintool screen that you have two Thunderbolt ports (XHC3) as well as the full compliment of USB2 and USB3 ports. Fine.
So, I've been looking through the SSDT-UIAC-VISION-D-V3.aml you were probably using before and can see certain ports have been left out to keep within the 15x port limit. This is great. In this file there is no HS13 configured. Now, looking at the unlimited ports we see in the latest Hackintool screen, you should realise that
no HS port above HS10 can have a USB3 equivalent. So HS11, HS12, HS13 and HS14 can
not be USB3 ports. The Z490 chipset just doesn't have them.
We can see you have identified the 4x USB3 back-panel Hub as SS07/HS07 so remember there is also a 4x-port USB2 hub that is
internal. Perhaps it was a port that has been discarded to keep within the limit?
Back to your main problem of USB3 ports not working properly. With the XhciPortLimit quirk active, I would now test each port with both a USB2 memory stick and a USB3 memory stick, just as if you were going to create a new configuration of your own, and see which ports you can identify for sure and their speeds.