Thanks ya'll for the kind words. I don't have time to overhaul the guide right now but I don't want to keep everyone waiting. I finally worked out a simple solution for the USB2 nightmare that El Cap brought. I won't be answering all the questions until I get a chance to update the guide.
Either clone your boot drive or install to a second drive.
Create your USB installer using the attached files.
Install the newest clover using the attached files.
Install OS X.
Install the newest clover to your El Capitan boot drive using the attached files.
Install the X79MacPro61SpeedStep.kext using kextbeast.
Use the "DSDT Stripper for Device SSDT.txt" to create your DSDT.
Run the AGDPfix.app and reboot. DONE.
I'll cover updating your current Yosemite later but if you know what you're doing, just make sure you delete all your old ACPI files and use these new ones. Also delete all the kext you installed including FakeSMC and except for the X79MacPro61SpeedStep.kext and update clover.
I will try to rewrite the guide soon but I need to get some sleep now.