Alright guys I managed to get Darkrai and Shaymin!
In PkHex, load up your save, go to SAV, Event Flags and then you need to go into Work Values and set all of the HAIHUEVENT_ID_X to 1.
Door to the Canalave Inn opened right up and was able to get Darkrai.
As for Shaymin, those flags should also allow you to trigger the event with Prof. Oak, but I just forced myself out-of-bounds using the Surf glitch.
Now, what the other 2 HAIHUEVENT_ID_X are, I have no idea. I would assume one is Arceus, but the last one? no clue.