I was checking with a colleague about your server's components hive and there seem to be a large number of components keys missing.
Was this installation slimmed or customized in any way?
If not, the quickest route at this point may be an 'in place upgrade' aka repair install of Server 2012.
If you have the extra physical resources, I would try cloning the VM and then attempting a repair install to note the results and what installation time to expect before trying it on the live VM.
Make sure the NIC on the clone isn't connected before powering it on to avoid conflicting with the production VM.
Is this something you would be willing to try?