I'd agree with what Ocarinaboy said but, I'd also like to add an option C. that the more I think about the more it makes sense to me.
C. The Goddesses sent people to the Mountain tops in Wind Waker, but if you think back to OoT the only mountain there really is in that game is Death Mountain. Obviously, there's a problem cause you got multiple Islands popping up all over the Great Sea that shouldn't be there, a prime example of this being the Forest Haven, and the Forbidden Woods. My idea would be that the Goddesses are responsible for all that happened with the Deku Tree rising to the top of the Ocean. He obviously plays a part in helping Link on his quest, and, the Goddesses knew that so they provided a way for him to be available, instead of being at the bottom of the big blue wet thing.
Also, the Forbidden Woods I always thought were the old Kokiri Forest cause you can find some of the Old Kokiri Houses. Forest Haven on the other hand, I believe to be the Deku Tree's Clearing, or if what Ocarinaboy said is correct, and the Deku Sprout was moved inside the Deku Tree in the flood, then it's Inside the Great Deku Tree, minus the top half of him.
Anyhoo, yeah. That's my take on it.