So I have a bit of a mixed update to report...
I've been running the flashed R9 280X in slot 1 driving an UHD 55" TV and the unflashed 7970 in slot 2 running the secondary LED Cinema Display. I've tested the computer with rendering, sitting idle, etc. and everything has mostly been fine. There was one day (2 days ago) when I let it sit for awhile and I came back and the computer was off. I didn't remember turning it off so I was like huh. I turned it back on and the fan on the 79790 wouldn't spin up nor would one of the two fans on the MSI R9 280X (the one closest to the I/O). So I thought hm that's not right and I removed the 7970 and put back in my 5870 to see if I fried anything.
Nope; it started right up and worked fine. So I tried the 7970 again and same problem, the fan won't turn on and one of the two fans on the R9 280X wouldn't turn on either. Then I tried a few more configurations. I tried the R9 280X in slot 2 by itself and it started fine. I also tried the 7970 in slot 1 (using logic board 6 pins) with the R9 280X in slot 2 using external power supply, and everything started fine. I monitored the machine and the processor usage of the 7970 was spiking a little higher than I was comfortable with while playing back a timeline in Final Cut Pro (7970 again running the LED Cinema Display and the R9 280 X running the primary UHD TV), so I didn't want to risk anything like the machine shutting down again (still not sure why that happened since I wasn't in the room... and if I remember correctly the machine was at idle and not rendering anything).
So I didn't fry anything but I did just take the 7970 out and am back to using the R9 280X by itself to drive both. My ideal config was 7970 in slot 2 running the LED Cinema Display, but now I can't seem to get the cards to start up properly in that configuration. I also can't figure out why the R9 280X in slot 1 would be affected by that setup (one ofd the fans won't turn on, it keep trying to and clicks but one of the two fans just won't spin up) when the card has no problems on its own. Reversing the slot order boots up and works fine but the levels spike a bit higher than I'm comfortable with given that the machine already shut itself down once.
I'm back to my old setup. It was a fun experiment I guess. Not sure what went wrong with it. I was switching cards so many times (10-20 times) that maybe that had something to do with it, because a few days ago before I really tried to get the 680 GTX to work the 7970 setup with the R9 280X was fine without issue and no shut-downs, and now I can't even get the fans to spin up. I can flash the GTX 680 but I'd kind of rather wait until next year for an RX 580 successor so I can do a proper upgrade.
That's my update folks. I'm here to answer any questions if you have them.