Well… I’m not a DB expert but those nested left joins look quite stressing for any server.
But if you like you can try with a different approach:
You can notice performance issues when you have mixed engines (move all MyISAM to InnoDB) or mixed charsets.
A mysqldump, edit your dump and recreate the DB is usually the best way to do those engine and charset changes… but feel free to try with ALTER table if you like (of course, remember to make a DB backup first 
).
Cheers,
m.