I tooks shots with all these commands to no avail. Of course, this comes after other things I tried, including deleting files I don't know much about, except they don't throw errors when they are deleted. The remaining errors, who knows?
The correct answer on how to recover starts with making snapshots of the server that can be used to roll back to a previous state. I have snapshots of the hosted domains, and snapshots of the backup server that has copies of the domain files, but no snapshots of the primary server. That is just stupid on my part, so I am fixing that.
Fortunately, this was a development server and I have the development environments fully restored on another server. I appreciate what I learned here about the commands you suggested.