This is quite amazing. Not just the brilliantly matched creepy music, which is still calm enough to let us think, but the slow-paced writing style, the clues and how they are all bound together. You give us an advice in the first clue and we have to use it in the last. Great. Also, thanks for the hints in the titles.
I can only imagine actually being there, all alone, in a dark room with a note scrawled over with letters; and using them to decrypt a final message, to have a final moment of realisation. Creepy - and awesome.
Also, I've just noticed your note about the secret ending - this kind of interesting easter eggs is something I love when they appear in a game - although sadly I wouldn't find this one if you hadn't told us about it. I will definitely be more cautious in the sequel - and yes, I do look forward to it. Good Luck :)