So this problem is fixed!! I am not 100% sure what did the trick, so I will post my solution here in case anybody else experiences a similar issue. I won't go into too much detail with these instructions as all the tools are here: http://forum.xda-developers.com/show....php?t=2612740
I first downgraded to the 1.15 hboot and radio. I had to rebootRUU and flash them there as it can't be done directly in fastboot as far as I know.
Do them one at a time (flash the hboot, then reboot-bootloader, then rebootRUU then flash the radio, then reboot bootloader again.)
After doing this I tried to run the RUU exe but it came up with an error that it could not update my phone, so I did the manual Alt 3.06 RUU.
This seemed to work great, restarted the phone and saw the stock rom. I then changed from superCID 11111111 back to the stock CID, relocked my bootloader went back to s-on status. At this point I ran the RUU.exe again just to make sure everything was as stock as could be.
Got that all finished, ran RumRunner again, installed CM11 and no reboot for nearly 24 hours. Pretty sure all is well!