Assuming you still have USBInjectAll.kext and XHCI-300-series-injector.kext installed, have disabled or removed the port limit patch in config.plist, and have a compiled SSDT-UIAC.aml file in /Volumes/EFI/EFI/Clover/ACPI/patched, I can only think of two reasons for a port not working; either you're trying to include more than 15 ports or you're trying to use one that you've excluded.