This was very well made, you've put a lot of effort into it, and I can only say that I hope you'll make more custom stories!
Here's my feedback(only meant to help you):
-The voice acting seems to start too late. I pick up a note, and you start reading at line 2 or 3? Is this a bug?
-Don't abuse the monster chase sounds. In the prison cells at the beginning, you hear the monster chasing sound in some rooms, I personally don't like this. I jumped behind a wall and sat there for a few minutes before realising there was nothing coming at me.
-A small thing that bugged me a bit was that in the lever room, all levers were in the exact opposite direction of what they were supposed to be. That's not very puzzling, is it?
-Even though the boss 'fight' was very creative and original, it took me quite some tries to beat. I like Amnesia for being different from other games, and I don't like the fear and atmospheric feeling making place for annoyance because I've died yet again.
-When getting stuck at the boss, I exited and loaded the game from an earlier point, but if you reload the boss map from an earlier point, you can't open the bar lock for some reason.
Apart from this, I loved everything. The lighting, mapping, everything was just great. Very creative use of 'holy items', sounds, recycling of items
(how you use the metal bucket twice), and more.