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Well, there must've been some room that you missed. A dungeon map and the compass help greatly. Just start from the rooms at the top of the swirling water vat, make your way down to the rooms in the middle, and finally the bottom. The middle is especially tricky.
(Is this a late post?)
That happened to me to. U missed a room. It's at the bottom of the swirling water room. I don't really remember what to do. If u need help, then put a MM Stradegy Guide on hold at the library, if one is avalible, just get it. Then go to the Great Bay Temple chapter, then find the place in it where u are in the game. Then that should help u! Hope I helped!