So from what I can tell it is the Plexguide install that is breaking the server. I can follow the above process and reboot the system 20 times and have no issue. as soon as I install plexguide it never comes back up. If you connect using the serial console it shows it stuck on boot up waiting for the mount to finish.
Hasn't been a plexguide issue for me. This error happens before I install plexguide and just do the reboot after mounting the nvme drives in raid 0.