Hi there. First off, awesome hack! Love it.
Secondly, I have a bug where Darkrai and all the other legendaries unlocked in Humilau Pokémon Center are unlocked right from the start. I am not sure if this has already been posted, as I don't really know what to search the thread for in order to find it.
It's funny though, right now I'm in the Strange House, and Darkrai is standing right on-top of the Lunar Wing (which is what I should have needed in order to unlock him)
Once again, awesome hack, and sorry if this bug has already been addressed...