I breezed this thread so if i'm off let me know.

For some reason could it be a GPU config? I doubt they were in crossfire config before but for some reason could the removal of one screw up the config as if there were two cards and I dunno try to overdrive 1?

If neither cooling solution from the cards was removed/altered and their fans/pumps are spinning I believe this to be totally on the MOBO or software side. Obviously remove any bridge/jumpers. If you haven't try to reconfigure the previous build where it was running "nominally". See if things are "aight". If they are maybe "disable" the card as much as possible while it's still physically installed, turn off 2nd gpu in all global apps (afterburner etc), turn off/uninstall device without removing said driver. Reboot, check things, if normall power down remove card. Boot, check things... this is where my trouble shooting needs input, I guess. I hope I'm not just rambling without any kind of perspective. Good luck.