Thank you for the response.
I am able to boot up off the 2016 Installation Media and get to a command prompt. From there I can run SFC and CHKDSK and they come back clean. Whenever I try to use the upgrade option to do an overlay I get the below message:
The computer started using the Windows installation media. Remove the installation media and restart your computer so that Windows starts normally. Then, insert the installation media and restart the upgrade.
Is there any other things I can run from the CLI options? For everything I've read lately it's hard to believe there isn't more hyper-v utilities to troubleshoot problems. The only thing I could find was powershells' repair-vm command that isn't what I need. We don't have the system manager in order to get access to the Repair-SCVirtualMachine commands either.