> How do you get rid of the bee? I cant seem to find it in any of the .pl files.

remove it from include/rules.html. it's not part of kareha.
people who have the admin password for your board keep adding it through the admin interface.

> Is there something i comment out to stop embedding of files?

yes. fix your php script so people can't inject perl code (so they can't just get the password again), and then change the admin password for your board.