I don't think I did, I remember doing it right. I just checked now, opening the respective files in the dispos/person editor with all of my changes intact and they showed up okay.
Edit: So I tried it again starting fresh from the extracted .3ds file, and I made sure the files were in the right places and when I rebuilt the .3ds again and pulled it up in Citra it was the same thing.
@DeathChaos25, I think you were right, I may have mixed them up somehow or something got a bit messed up because I just did a really simple change (turned all the fighters into cavaliers) and it loaded just fine. I'll start from scratch again and see where it goes.