Oh dear....this is what I really didn't like about the game: story completion.

BUY A GUIDE

That's all I can tell you really. If you didn't know there are multiple endings, and you have to get 100% to see the last scene. The normal ending SUCKS EGGS. 99.9% won't cut it, and by the sound of it, you're waaaaaay below that. The best I've been able to do is 96% and I had a guide, following it as closely as I could. I got to chapter five and realized I screwed something up waaaaay back in chapter one, and I was like, NOOOOOOOOOOOOOOOOOOOOOOOOOO!!!
I missed out on the mascot dressphere (which you get by having every location a hotspot in chapter five) and I didn't get the bonus scene at the end. (Though I did get a good ending at least). Most dresspheres are only available by preforming small actions, and screwing something up in chapter one will prevent you from getting a sphere in chapter five. If you're at chapter five, it's too late to get most of them. I would reccomend starting over, or trying to beat it with what you can get and trying your luck with the New Game Plus.