Is there anyway I can convert a full populated MyISAM database to InnoDB (in a way that will create all foreign key contraints, same way it would be if I ran the syncdb command
This really has nothing to do with Django. It's entirely a MySQL thing, and there's documentation on just this type of thing directly from them: http://dev.mysql.com/doc/refman/5.5/en/converting-tables-to-innodb.html