Not to rain on your parade, but literally 90% of the Japanese text in this game is encrypted. PokeStation is working on a full translation that will include the encrypted story text: http://forums.pokestation.net/showthread.php?13925-Translation-project-for-Pokemon-x-Nobunaga-s-Ambition
If you decide not to finish your translation, then please consider contributing your files to PokeStation's translation.