Just finished the book (picked it up on a bookstore date last Friday). Holy shit on a biscuit, that was a/n amazing/confusing/recursive/terrifying/disturbing piece of fiction. I'd almost like to say that watching Johnny fall apart at the seams was scarrier than the House on Ash Tree Lane. Then I remember exactly how disturbing I found the quarter-inch discrepancy.
This actually reminds me strongly of (though in reality, the influence is almost certainly in reverse) John Dies At the End. The core idea that all it takes is one impossible thing, one truly impossible thing, undeniably in front of you, to completely destroy your life and everything you care about is present in both works. The difference is that JDATE is played for laughs and branches out it's horror content substantially, while House of Leaves is (subtle mocking of academia and Tom's whistling in the dark joking aside) played straight and entirely focused on two elements: The House itself, and (indirectly) the Minotaur. One of things that occurred to me while I was reading it was that when Johnny Truant slips into his psychotic episodes (particularly when he fights Gdansk Man), his thinking process becomes incredibly simple, animal-like, and reminiscent of a certain Household Guardian. I believe there was even a mention of him 'growling' or 'shouting' at the girl (forget her name) and stopping her from coming closer.
Since the Minotaur was stalking him and apparently killed Zampano, it's quite possible that the Minotaur is the corrupting influence of the House (and/or possibly the book) on the people around it. The House (or it's guardian) crippled Navidson, killed every single person who initially set about trying to explore it, killed one of the people who set about documenting it, and drove the other nuts (possibly turning him into the Minotaur in the process. In fact, you could argue that it did the same to Holloway.
My best guess is that the book itself (which occurs in both layers of the narrative, and the real world) is another form of the House. The House on Ash Tree Lane may or may not have existed in the universe that the book takes place in, or it could be the book (fictional)'s interpretation of itself (hell, it's recursive enough as it stands).
Anyway, I'm rambling now, so I'm going to go away.
I can kill you with my brain.