On the telephone, the killer tells Peter Neal that "you wrote those words, page 46," but in fact the words quoted would have had to be on an odd-numbered page of the book TENEBRAE, given the placement of the text we see in the opening sequence. See more
I've been charged, I've tried building a plot the same way you have. I've tried to figure it out; but, I just have this hunch that something is missing, a tiny piece of the jigsaw. Somebody who should be dead is alive, or somebody who should be alive is already dead.
You know, there's a sentence in a Conan Doyle book, "When you have eliminated the impossible, whatever remains, however improbable, must be the truth."