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I don't have any experience with music in general, but regarding .midi to .s files, I always assumed it happened simply by making the ROM, much like .png to .4bpp or .pal to .gbapal. Shot in the dark, but can you not simply add the new songs to the songs.mk file?
Did you change the struct for BoxPokemon in include/pokemon.h to have EVs as more than a single byte? Note that simply changing it from u8 to u16 will increase the size of every BoxPokemon in the game causing all sorts of problems, so you should rearrange the struct to save bytes. After this...
Even if you are not using pokeemerald, it can help with questions like these. You can look in include/constants/flags.h to see a list of the flags in the vanilla game. A sizable chunk of them as unused.
Am I missing something obvious, or does the region map editor not change the region map and tilemaps within graphics/interface? It appears to only change the graphics/pokenav folder. This results in the pokedex area screen keeping the Hoenn map. I hope I'm missing something simple. Thanks!