@kgp thanks for your help.
I'll try to explain better my problem.
I could not get the usb ports to work correctly following this guide.
Following the guide, with your config.plist and DSDT patches in Clover's config enabled and without any SSDT from the repository, I got only one usb port working (the one next to usb-c that is attached to AsMedia's 3.1 gen2 controller). I'm running a vanilla install on High Sierra 10.13.6.
You can see this in IORegistryExplorer:
So, right now:
2x usb 3.1 gen 2 from AsMedia (one is type A and one is type C) --> the type A is working and I suspect that also the type C is working
4x usb 3.1 gen 1 from x299 chipset --> not working
2x usb 2.0 from x299 chipset --> not working
By "not working" I mean that devices are not powered on (my pendrive didn't blink and my keyboard did not show nor caps lock nor numpad leds).
This morning I tried to patch the DSDT manually without using your clover's patch but as I said I could not get my system to boot.
At this point I'm asking how you got usb in your motherboard, I think that x299 Deluxe and x299 Prime share the same intel usb controller, so I should fix the problem in the way you fixed.
Also if anyone has my exact motherboard, the Asus X299 Prime, please contact me.