While that package is unzipping, I can help you with the issue you mention about the unused files. Here is what you do:
Check all you plugins, one by one. Some of those will use sound files or graphics.
Now make an event on a map the player will never see, and make all those files be triggered by this event. You can use "Change Actor Image" for all face files, character files and SV battlers. You can use "Show Picture" for loose pictures. And "Play BMG/BGS/ME/SE" for audio.
Now deploy "exclude unused files" and everything should be included.