Here's something that it seems everybody's been overlooking (so far in this thread), you have to watch every story sequence, and you have to listen to Maechen when you reach the Youth League HQ at the beginning but you CANNOT interrupt him even if the game gives you the option to. When the selection comes up, do nothing until he continues his story (can't remember 100% if it actually just continues if you leave it be, but it does sound accurate). His story can be painfully long, but you must endure if you want that 100%. And what I meant by watching every story sequence, is that you must not press any buttons to "speed up" that part of the story/game, including every (dress)sphere you get. Just sit back, relax, and enjoy the FMV, or the narration or dialogue or whatever that occurs on the screen. If you were able to get 99% on your second play-through, those little nit-picky things may be the reason why you didn't score 100%.