Yeesh, I just finished this. The real story is pretty interesting, and the fragments of the story told in each 'route' are interesting too. If it was made by Shinachiku-Castella it would be a nice gutwrenching lewd game. Ruined by lack of assets and atrocious pacing/gameplay loop.
If you want the story, start from File 4, I think. Files 5-9 are different parts of the true ending. You're supposed to follow the ?'s, open the chests in the house in Center and Eastern Districts, go to the abandoned house in south Eastern, then go to the pink haired guy in Western District, back to the cave, then the guild, and finally either leave the village or to the church.
File 10 is post-game, though you see past h-scenes from the Church (endings) and Key Item (parts 1-5).