make backup of kext AppleGraphicsControl.kext before running that script, then run the script, then restore that kext from backup.
This will give you cuda but no output from 980ti.
if that works, you can donate me via link on http://netkas.org
basically what that scripts modifies in AppleGraphicsDevicePolicy.kext (which is inside of AppeGraphicsControl.kext) is not good for retina imac, it breaks OSX ability to use MST screen on 5k imac, so you getting only half of screen output.
The author of that script isn't very smart.
I recently built an eGPU with a GTX 980, and connected to a 5k iMac. After trying instructions on MacRumors on how to get it working in OS X, and those software hacks did not get it working (non-EFI) I stumbled upon this forum and the automatic-eGPU script. I ran the script and after a reboot my 5k had the same problem as of OP...I uninstalled the script, backed up the kext, and ran the script again. After rebooting the 5k was still showing a small square picture, while my Dell Ultrasharp 1440p fully worked connected to the 980. When I started to replace the kext that I backed up both screens turned off. I softly pressed the power button and it immediately turned back on (it likely went to sleep even though I have that disabled), only this time the 5k was back to normal (3200x1800). so it seems to me that the script was improved recently.
Now if only I can get it to work in Windows...I tried this first and the drivers seem to have been clashing (nVidia and AMD). The picture was mirrored to both displays even though they were using different video cards. I fiddled with the very limited settings for a while and the 5k turned off. I went to reboot and got a sad face
. So now I can only boot into Windows with eGPU unplugged.