I have the essentially the same setup that you have and I had those very same problems. In fact, for a while there I was going to go postal on the firefox people because it kept freezing whenever I closed a tab or two and I could not believe that this was happening in a Mac Pro! I had times when processor usage was at 2% and the screen was frozen and I could not use mission control; more than puzzling, the experience was disturbing: was my Mac Pro suddenly OLD!? Then, I saw the same current version of firefox running on a 2013 Mac Pro and no such problem; tried mission control and the response was more than instantaneous! While I had already decided that I needed to change the video card (an electronic text with 6000 pages took long enough to open that I could go and do other things -what people with lesser machines do, I can't say.) that experienced clinched the decision. The immediate implication was that the GT120 is simply not up to the task of the significant increase in rendering that El Capitan is passing on to the video card. For what I do, the GT120 was more than enough because UNIX (and OS X then) does not demand much of video cards; however, while OS X remains a POSIX compliant UNIX, the NeXT heritage allows/facilitates some changes in so far as video rendering that make Metal possible. The upside for Apple is more gamers and more frequent upgrades of enterprise iMacs.
My Mac Pro has had the Sapphire R9 280 Dual X (6+6) but (2x DVI, HDMI, DP -not a typo, full size, not mini) which I've been told in another thread is less than desirable. The difference is extraordinary and it is not just limited to eTexts, video rendering is near 50 fps and subjectively, WOW! What makes all the differences more dramatic still is that I have not done the resistor surgery yet!! This card will support UltraHD so I can only imagine what it would look like if I had a 5k capable monitor! The only problem so far is that the instructions inside leave much to be desired; there is nothing that says which position of the push button switch is Legacy and which is uEFI.
I had a plan: I would leave the GT120 in and use my monitors multi-input capabilities to do the boot screen when I needed to...no dice, the machine would keep logging me out the second I did anything other than stare. Taking the GT120 out solved that problem (during that time, the system report saw two GT120s for some obtuse reason!) and system reports the card as native 7950! somewhat crazy since there is still no boot screen!
Even if I did not do anything else, for $200, this card is more than fantastic considering the price of what must be the same exact card from Sapphire but sold for the Mac which is ~ $500. I am very happy with this card and happily recommend it. Also, given how much has been said about noisy video cards in these forums and elsewhere, I was concerned that I would end up sitting next to a jet engine; however, the card is surprisingly quiet and the temperature would seem to hover around 20 degrees above ambient.