JH191:
I have the HD 4870 in my system. It worked well with 10.11.1 but not 10.11.2 for some reason.
I was unable to get to the login screen at all even with safe mode boot up.
At that time I was using multiple monitors hooked to the HD 4870 and another hooked to an HD 2600.
I read some reviews and it seems El Capitan generally has problems with multiple monitors.
From my personal experience, El Capitan has changed things on the graphics card driver front.
While it used to be generally true Apple provided the graphics drivers.
I don't know if Apple is going to support the older graphics cards anymore.
I am probably going to switch to two NVIDIA GT120s that I have from another Mac Pro.
NVIDIA is at least pushing out new graphics drivers for the GT120 and 10.11.2.
Good luck.