The Shin'ou Pokédex Order is stored in two files: data/poketool/pokezukan.narc and data/poketool/shinzukan.narc. Like other NARC files, these files are wrapped in the NARC file format.
The format of the contents of pokezukan.narc is simply an array of 494 shorts indexed to National Dex Order (Bulbasaur at index 0x01 not index 0x00) with the value of the short being the Shin'ou Dex number of the breed of the Pokémon. Note that if the Pokémon is not in the 151 entries in the Shin'ou Dex, it maps to 0x0000.
Shinzukan.narc is the opposite of pokezukan.narc. The format of the contents of shinzukan.narc is simply an array of 151 shorts indexed to Shin'ou Dex Order (Shin'ou Dex #001 corresponding to index 0x00) with the value of the short being the National Dex number of the breed of the Pokémon.