Well, I've never used RM Tool before, but I've heard of these errors/problems that others get (most notably the one that you mentioned where it deletes files you are using in your project). I would just suggest you do it manually (even though you've said it would take a long time). Start with the MP3s that you aren't using (that is, if you use MP3s), as they usually make up a majority of a game's file size. Trust me, it's worth it (I wouldn't leave my project to the hands of some program anyways).