Thanks to a good portion of your guide I'm currently booted from my 10.11.5 SSD with:
i7 5820K @ 4.2 GHz
Gigabyte GA-X99-UD3P
GTX 980 Ti
32GB RAM
There are currently a few issues...
1) It boots when it feels like it. Sometimes I get the AptioFix2Drv error, sometimes I don't and it boots fine. No changes in the config or Clover boot arguments.
2) The Mac Pro definition didn't work so I kept it as iMac 14,2. In fact, the only way I could boot from the actual SSD/installation was to copy everything from my Clover USB (plist, ssdt, kexts, drivers) to my SSD's EFI.
3) USB 3.0 does not show up, only USB 2.0. (related to above?)
4) I can't find this "Test2.efi" you're referring to in any of the posts so I'm unable to install additional PCIe devices.