Thanks for the suggestion, Jeremy.  I ended just restoring everything but the databases with tklbam, and was lucky enough to have a pretty recent SQL dump on another system.  Using the mysql commandline tools worked fine, even when tklbam continued to complain about packet size (I'd tried editing both via webmin and vim'ing my.cnf directly, then restarting).

So far, every time I've really been in a jam, tklbam hasn't worked for me.  Twice I've had systems run out of disk space, and there wasn't enough room to restore, and this time it was mysql and the packet business.  I guess I'll switch back to snapshots/rsync/manual mysql dumps.

Relatedly, root can no longer log into phpmyadmin, even though it works fine on the command line (mysql -u root -p).  Dunno what happened there, or what tklbam may not have restored.  Maybe the mysql management tables themselves are still fubar, but tklbam won't restore them, so I don't know what to do about that.  I'm perfectly comfortable using the command line mysql client, but I'm concerned about data corruption.

I would love it if tklbam had some kind of extract command, where you could give it a backup id and date, then just pull specific files out, so I could nab just the mysql.* tables and restore them.