although i am not sure anymore after passing the barrier of a million changes in my system, i'd say GPU first > boot (with nv_disable if needed) > install driver > reboot > CC change > reboot > pray to whatever you believe the most....
I think I am about out of ideas... in the past 24 hours I've done the following:
Basic install of OS 10.11.6, using Unibeast.. resulting in 15G1011 install
Cloned this install to another drive, using SuperDuper... manually copied EFI partition
Updated OS to 15G22010 (to be directly compatible with the nVidia driver that I found
Found that nVidia driver is supposedly for Mac Pro versions 3,1 and 4,1 and 5,1
Changed Mac model to 3,1, using Multicast
Installed nVidia 346.03.15F16. pkg and CUDA 8.0.90 (the latest iteration of CUDA that is still compatible with OS 10.11
Reboot - CUDA says "No GPU Detected"
In Clover Configurator > System Parameters > Checked "Nvidia Web"
Reboot > CUDA says "No GPU Detected"
In Clover Configurator > Boot > Checked "Nada_Drv'1"
Reboot> CUDA says "No GPU Detected"
Rechecked BIOS > "Initial Graphics = PCIe 1"
Updated Clover to Version 4741
In Clover Configurator > Changed " NV_Drv=1" to "NV_Disable=1"
Reboot
Disable SIP Fully (in RT Variables > CSRActiveConfig > Changed from Ox3 to Ox67
Install Lilo.kext
Reboot
"No GPU Detected"
Install Lilo.kext and whatevergreen.kext (supposedly the updated version of nVidiaFix)
Uninstalled all nVidia drivers and CUDA
Physically removed GPU (Based on a YouTube video I found that specifically dealt with El Capitan and GeForce 970)
Installed nVidia driver and CUDA
In Clover Configurator > Boot > Clicked on "Verbose" and "Nvda_Drv=1"
Reinstalled GPU
Reboot
"No GPU Detected"
I've made two incremental clones of the boot drive to get to this point. I also thought that maybe I could try to install Sierra, but when I created the install/Unibeast USB, it would attempt to boot into the Mac OS, but would stall at about 10% of the progress bar, and revert back to the BIOS window.
Any suggestions will be greatly appreciated. I've about run out of things to research on YouTube, TonyMacX86, or anywhere else... ??????