I'm experiencing the same problems on a fresh 10.11.3 install running on a Skylake-based system with iMac17,1 as System Definition. Did the same steps as you, copy, overwrite but no avail. I'm using a GTX 970 and connecting my U2515H via Displayport, but shouldn't give an error. It's quite strange that nobody is experiencing problems like these.
For me it's a gtx960 with also a screen on DP, i7-6700k.
I'll just wait for them to release a driver update or osx 10.11.4 at this point.
Nothing seems to help or solve it.
Sometimes it acts up when doing a copy replace. Copy to desktop the vanila 10.11.3 kext, modify it, delete the original kext from s/l/e, then copy the .kext back with your fave kext utility. I have had times in the past where just overwriting using a kext utility doesn't work.