Instead of explaining away the apparent inconsistencies, what I should have done was to simply fix them either by getting rid of them or by better explaining them within the story itself so as not to confuse subsequent readers. To all the prospective writers out there, take heed: thinking that the reader understands your prose (or should understand it) as well as you is a common rookie-mistake. One might call it the "mistaken assumption of there being a telepathic reader" (I mentioned this some time ago on the TML, back on Feb 19, 2013 Re: [TML] A Review Of Dorsai!).
It sort of reminds me of being in a math class, and the professor writes some complex expression on the board, then skips about 8 or 10 steps to solve for x, turning around to the class with a conclusion that, to him, is self-evident. "The proof is trivial," he says, moving on to a different topic. Well, it might be trivial for him, but it's not for me.
Similarly, for a writer to expect that a prospective reader is going to be as intimately familiar with a novel as himself so as to be able to understand whatever the writer is hinting at in any given scene... it's arrogant and lazy on the writer's part. I strongly suspect that the comments and questions you emailed me were pure gold, and I should have made much better use of them than I did. If I ever get around to doing a rewrite, I hope you'll permit me to run the revised text by you for a second round of comments, as readers like you are a treasure.