I don't know if any of this can be useful or if it was already known, but I'll post it anyway.
I've made a list of the Pokémon species IDs in Gates to Infinity. The only places I've seen them being used are the RAM and menu_ground_chara_select.lua, but I assume there's more than that. The same order seems to be used in pokemon_data_info.bin, which is similar to the one found in Super documented earlier in the thread. http://pastebin.com/iahAZvA8
I've looked at dungeon/random_parts.bin some time ago. It has a simple structure, figuring out how it works isn't hard, but I have yet to see anyone talking about it.
random_parts.ent is a list of pointers to the start of each SIR0 in random_parts.bin. Starting from byte 0x10 of random_parts.bin there are 0xA4 bytes of data, then 0xC of zeros, and then it repeats. Every 0xA4 section represents a part of the map formed by 9x9 tiles, two bytes for each tile. The game rotates and arranges the parts togheter in a way that makes sense. Each DLC dungeon also has its own random_parts.bin file, which should mean they can have their own layouts. random_parts.bin only controls a tile's behaviour and the map. The model doesn't change, I assume there's a part of the file that says what model each 0xA4 section should use. [Edit: That's not the case, the file only contains the various 9x9 blocks] At 0x1134 there are 0x16c zeros, at 0x13F4 there are 0xBC zeros. http://pastebin.com/K4V0i4Kk
The file can also be found in Super, but I don't think the game uses it [Edit: It is in some dungeons, like Heart Lake for instance, and it's probably used in RTDX as well]. I tried it in GtI and it only works for the first few dungeons (later ones just crash the game), probably because it's shorter than the original.
