rob1980, here's exactly what I did:
- moved ACPIBacklight.kext, ACPIBatteryManager.kext, ACPIPoller.kext, AppleIntelE1000e.kext, FakeSMC.kext, GenericUSBXHCI.kext, HSSDBlockStorage.kext, IOath3kfrmwr.kext, JMB38X.kext, ProBookARPT.kext, RealtekRTL8111.kext, VoodooPS2Controller.kext from /S/L/E/ to /EFI/EFI/CLOVER/kexts/10.9/ (moved, not copied - meaning these kexts are no longer present in /S/L/E/)
- replaced AppleIntelCPUPowerManagement.kext and AppleIntelSNBGraphicsFB.kext with vanilla (from the installation usb) ones, same for AppleHDA.kext
- added patch for AppleHDA to Clover (and therefore created AppleHDAITD with some .zlib files from the patched applehda kext, just as per nguyenmac's guide)
- didn't do anything with AppleRTC
- made sure InjectKexts is set to Detect in Clover's config (this way it checks whether FakeSMC is present in /S/L/E/ - if not, Clover injects all the kexts from its directory)
- repaired permissions, rebuilt cache
and it works, there's an extra second added at the very beginning of the boot (HDD indicator light starts with a 1s delay, that's how I can notice it) but everything else seems just OK. I guess this is the time when Clover actually injects the kexts...
I'm sorry you've got problems mate, I'll do my best to help you.