Yes, the link is done directly in the admin panel. That was easy.
The logo is part of the theme and each theme is separate. AM found an extenssion that can automatically correct _many_ of the third-party themes, but isn't guaranteed to do all of them. Attempting to install the extension exposed some other issues left over from the upgrade. (The database conversion got borked during the upgrade. I had restored the database and run the upgrade again, just for grins. It died in the same place. Surprising, huh?
A thread on the phpBB forum gave some possible solutions but I haven't had the time to try them yet; they're a little involved. I was hoping to do it this weekend, but no luck. I'll get to them tomorrow after work...)
Then, I'll try the extension again and we'll see if it can do the styles I've installed; I'll do any others "manually". Since the logo being messed up doesn't hurt the functionality of the board, it's been lower priority than the database cleanup...