Thank you so much for the comment, basis! I really appreciate it, and I'm sorry it's taken so long for me reply. I simply don't stop by here as often as I should.
It's also absolutely okay to ask questions. Unfortunately, some of your questions cut directly to central mysteries in the story, so I won't be able to answer everything. I'll do my best to answer what I can, though.
Overall, one of my goals was to write a story with a somewhat naturalistic approach to mysteries, in which a number of details remain hidden and no single character has the entire picture. While I think I was somewhat successful at this, the side-effect is that a high proportion of readers are hitting the end and scratching their heads.
There are ways to frame a mystery so that the reader is at least aware of what they aren't supposed to know (known unknowns, so to speak), and that's something I need to work on. This was my first novel, and I hope to do a better of job of that in the future.
Anyway, thank you so much for your interest, and I hope this helped clear things up. Cheers!