For some reason, the last few files, (ssbb main theme and FFIX battle theme for example), don't seem to work, my Finale program says that the file is incomplete. I'm not sure if there's a problem with my program or with the songs, any advice would be appreciated
Your version of finale is possibly older than those that the files were created with. For example, if you have a 2009 version, and they were made in Finale 2010, then it won't work.
I haven't checked the files, but I'd be willing to bet this is the culprit.