Hello. I was also trying to make HD Graphics P4000 of an E3-1245v2 work. On an Asus P8C WS and running El Capitan and Clover r4522. Now I succeeded by putting the correct FakeID into Clover config.plist and putting the FakePCIID.kext and FakePCIID_Intel_HD_Graphics.kext into EFI/CLOVER/kexts/10.11 (where I have all the other kexts also).
And. All the keys that have a hash, i.e. '#' before them, are disabled in the default config produced by the installer. Good luck.