Similar problems with a EVGA GTX 750 Ti. I originally installed El Capitan on my system with a GTS 250 card and as long as I booted with the installation USB drive, everything but USB 3 worked perfectly. My monitor died so I decided to get a 4k monitor and needed a more powerful card to run it. After installation I had the usual problems, no hardware acceleration, choppy video, etc. I tried all the suggestions in this thread; Booting with nv_disable=1, installing the web drivers, then re-booting after enabling nada_drv=1 and making sure that injection is not on. I still do not have hardware acceleration and have all the same problems. Also, the System Profiler shows the proper card but with no memory. In a strange twist, as I was installing the drivers I updated Clover in the working drive and was finally able to boot it without using the install drive. However, now the graphics appear to be maybe 1020X768, instead of the native 1980X1020. All settings in Clover Configurator appear to show 1980x1020, and when I check the resolution in Display Preferences it shows 1980x1020, and the system profiler shows no card. Booting up using the install drive brings everything back.
I have enclosed both config.plists. I am using the DVI port on the card.