I'm able to now get the two MySQL servers running at the same time, and I think I have the user databases imported correctly, but it still doesn't work.

When I shut down the "old" v3.23.43 MySQL server and start the new v4.1.13 in its place, the databases seem to be there, but the websites that use the database hate it.

The MySQL database security has changed, and I didn't restore that data to the databases, but I did go through the old backup and try to create the new data with roughly the same permissions; that is, each user can use their database, but not other databases.

I've returned the "old" v3 server to operations for now, but I'm not done yet!