After going down too many roads to recount here, I was able to return my server to using mysql 5.7 and I will just leave it at that for now. Shout out to Danny who helped me out.
In the end, I completely reinstalled mysql. Then I placed a backup of my /var/lib/mysql folder back in place at /var/lib/mysql. It appears that with active courses and new courses, things are working.
However now when I unarchive an old course, it has database structure errors and won't initially load. I can use the admin course to update the course I unarchived. But the course has lost its users and problem sets. I had to use the command line wwsh to add myself back into the course, where I can get in to see that these things are missing. Files form the course are still there, it's just the database elements that are gone.
A less concerning issue is that I seem to not be able to use extended characters. I tried creating a course where the title had an em dash — in its title. There was no error, but then that course's title appeared with some accented letter a in place of the em dash. So character encoding is not behaving as hoped for.