If you want to go that route, I would remove EVERYTHING from the resource folders - apart from the img/system folder. Then go through the System tab and determine what sounds, images, etc you want and add those. Then go through the Animations tab and decide which ones you want to keep, and add the animation images and the SE that they use. If you're going to scrub the database and put all your own stuff in there, you can leave it at that. But if you want to use stuff from the default database, go through and determine what resources they need and add those.
From there it's just a matter of adding things as you need them. The you'll know your project will ONLY contain the things you really need.
On the music, put in both the ogg and the m4a versions. When you export, it WILL only use the file for the platform you choose.