Where were your source files from? PSX, Saturn, or PC? Not sure, but it may make a difference.
I used my own Playstation disk to generate all my files (following the available guides), and the only files I had issues with were the audio tracks (which I remedied by using the ones made available, which I think were linked in one of the 'issues' threads on github).
I've not got my 3ds to hand right now, so I can't specifically say how I've got it set up, but I'll check when I get home and provide a screenshot or something unless someone else is able to help in the meantime.