Finally got around to doing some work on my server rack and machines. After nearly 2 years of up-time I realized 6 of 8 fans were either grinding or not spinning at all. Ordered Noctua replacement 80mm/40mm replacement fans with SSO2 bearings which are very quiet and have high airflow.
Phase one of updates, shutdown ESXI host which accounted for service/site downtime today. Cleaned out the machine and replaced all intake fans as well as hot swap bay fan. Clonezilla copy of the original USB stick with ESXI failed, server would not boot off the cloned USB. Used the ESX CLI and exported the configuration file. I then proceeded to do a fresh installation of ESXI 5.1 799733 and imported the backup configuration successfully. OS now working off a brand new 16GB Sandisk USB stick. Patched to ESXI 5.1 Update 2 1483097 and all VMs have recovered successfully.
Phase two to commence over the next day or so. Storage NAS will be taken offline for cleaning and fan replacement which will account for Plex and Subsonic downtime. Currently running a backup of 8TB of data to external USB disks before proceeding.