FakePCIID_XHCIMux.kext is part of RehabMan's FakePCIID. You will need this one only if you have a problem with some internal USB devices and if you are in temptation to use USBInjectAll.kext to resolve those issues. In that case use FakePCIID_XHCIMux instead, otherwise you do not need it.
You do not need EAPDFix anymore. AppleALC is enough now.
Since you are using WhateveGreen, remove Shiki. You can also use this patch instead of IntelGraphicsDVMTFixup