Update I upgraded my cloned drive to El Cap, and had a little trouble booting it. Clover hadn't installed correctly (or maybe i didn't install it correctly
) So I mounted the EFI on my El Cap drive and placed a copy of Unibeasts USB EFI folder on it. It then booted.
I've now got a couple of issues
1) USB not always working for keyboard/mouse etc(Power Issue?) cause unplugging my mouse from the mac keyboard and trying the same usb slot, it works for the mouse.
2) CPU not showing the correct Bus Freq (cosmetic I think)
3) GPU reporting the wrong slot (Cosmetic, but my dsdt is saying Slot-1 and System Overview is saying slot-0)
4) Memory slots showing as Dimm1 to Dimm6. Yosemite shows these as Banks0/1/A0 to Banks10/11/A5 (Don't know which is correct but they work so Cosmetic again) I used Clover Configurator and selected XMPDetection=Yes this now shows the correct memory Freq/DDR3 etc.
5) Restart hangs sometimes, possibly the same for shutdown.
As long as my external harddrives are plugged in before boot, then they work. I use a USB3 card which shows as USB 3.0 SuperSpeed Bus in Yosemite but under EL Cap its just USB3 it doesn't run at USB 3 speeds either. The drivers used are different.
ElCap uses Host Controller Driver: AppleUSBXHCIFL1100 and Yosemite uses Host Controller Driver: AppleUSBXHCI.
My dsdt only contains two extra settings 1) The GPU has been added 2) The Processor has also been added. Otherwise its the standard ga-x58a-oc from this site.
What has surprised me is that my Geekbench score has went up 400 points under El Cap to 10646. Yosemite was around 10200.
If I can get usb working correctly then I will upgrade my Yosemite drive but for now this was just a test to see how far I'm off from having a fully working system.