How do I revert all of my DB tables from MyISAM back to InnoDB?
The easiest way is to take a backup with Backup and Migrate, open it in an editor and search/replace "MyISAM" to "InnoDB".  Then restore it.

Personally, I would restore to a new catalog, and then switch the database in settings.php.  This way, you can test before making the new version live.

Otherwise, this is a dup of How do I convert a database from MyISAM to InnoDB?