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Solved the issue, or at least some of it.
The problem was related to the service account originally being used by the McAfee Epo server service to access the SQL database being locked out in active directory (mistyped password for a scheduled task).
Unlocking the account allowed us to restart the server service and we now appear to have full functionality again on the EPO side. However, there is still no SQL servers listed in the CfgNaiMS.exe SQL server dropdown menu. I'm a little worried if this means database corruption, but haven't been able to find anything out of the ordinary on the SQL server / database.