So far what I've seen is cutscenes mostly happen with a If Gamemoment= variable, so I just got it to disable in that field if it's that time. I think that'll be fine for now.
I managed to fix the issue coming from the world map, it's set up so that if you come from any other map that wasn't defined in the variables above (any of the others locations that you can walk into), it'll load them on the stairs. I had to use Otyugh to work out the coordinates and the triangle ID. DLPB, you are a hero
I'm also setting it up in such a way that any character can be the leader in Cosmo Canyon, in some cases rearranging scripts.
Once I've done all of Cosmo Canyon, I'll upload it for you to look at/implement in your own work.