Hello there.
A couple of things to note about your set-up:
1) You have duplicates of some kexts in System/Library/Extensions = USBPorts, USBInjectAll, XHCI-unsupported, and also FakePCIID*.*. Remove them from there. If you really want to duplicate any kexts then I would recommend they go in Library/Extensions NOT S/L/E. Basically no third-party kexts go in S/L/E
2) You have a Lilu.kext in CLOVER/kexts but nothing to partner it with. I couldn't see anything in S/L/E either. Anyway, if there is, and I just couldn't see it, move the other kext to CLOVER/kexts too.
3) Once you have created the aml and kext you shouldn't need the three port-limit removal patches any more.
4) Check IORegistryExplorer for the EH01/2 or XHC tree sections to see if your ports are showing.
Let us know.