What the Hell! You can't do that. Just add a CT timeline in there and you could summarize your beliefs as: I believe there is a timeline. You're so indecisive. LOL
About the darkness, could not a similar phenomenon have happened in the adult half of OoT? Darkness poured out of the temples, gateways to the Sacred Realm. If FSA Ganon was in the woods when he first made his way into the DW that would explain why the Darkness is centered there. Also, when looking at the Woods in FSA there are few other places where the Moon Gates play such a large role.