I find out that the legendary birds are found in a different way to the games. Let's say you want to summon Articuno. Just craft an orb of frozen souls, fill it up over the course of a few battles and offer it on the ice shrine. ...Yeah, I'm thinking no. *clutches Bible*
So I figure "Why not just add the areas you normally find them in as generated structures?" So I find that a mod called Recurrent Complex allows you to build, export and import your own custom generated structures.
I've already gotten most of the building done for the abandoned power plant. But how do I control what pokemon can spawn in it? How do I make sure that the player will be able to encounter Zapdos when they get to the final room?