OS X 10.10.4 update on 2009 Mac Pro: stuck at "Missing bluetooth controller transport" on boot
I'd certainly try it with only one of the GPUs in there, try swapping over if no joy.

I'd also be tempted to run the "standard toolkit" assuming you can get into the OS fully, though the first can be done from the Recovery partition…


Reset the SMC
Shut down the computer.  Unplug the mains power from the back &amp; leave for 15 seconds. Plug back in &amp; wait another 5. Boot.
Reset the NVRAM
At the boot chimes, hold  Cmd ⌘   Opt ⌥   P   R 
Keep holding all 4 keys until you hear the chimes again, then release.
Fix permissions, Verify &amp; if necessary Repair disk, using Disk Utility, from Recovery if you still can't fully boot - 
 Cmd ⌘   R  at the chimes.


If that does allow you to boot…


Reset Home folder permissions &amp; ACLs using OnyX  - Maintenance tab/permissions, tick the box at the top then Execute.
Update to 10.10.5 using the 10.10.5 combo update, not the delta from App Store


Being a Mac Pro you always have the option of just dropping in a new drive &amp; putting a clean OS on there, from which you can poke &amp; prod at the other drive with impunity.
There's also, of course, the option of then migrating a Time Machine backup to that new drive &amp; simply discarding or repurposing the old one.