..... I was left nearly speechless for a good few minutes after reading this thread, the two above, and more that you've posted.
After having read a large portion of your material, I can now see why you're so convinced of your own theories. You make extremely strongly supported arguments in each and every one of them. It's honestly (even for me) exceedingly difficult to make any counter arguments.
Everything in my being wants to find everything wrong with your theories and expose them (playing the devil's advocate for good sport, of course), but you leave too few holes unfilled for me to do so. For this, I applaud you. You have gained a great deal of my respect by exemplifying such diligence and thoroughness, which are virtues that I value greatly.
Unfortunately, I'm quite bothered by the fact that you still claim certain aspects of your theories to be "logical certainties" when defending your views. Until Kishimoto proves you right, your theories are all still nothing more than educated guesses. Albeit, they are the best theories for any work of fiction I've ever seen on the internet... and I really do think that Kishimoto will prove you to be right. He'd be out of his mind not to based on everything you've compiled revealing what he's seemingly demonstrated time and time again throughout the manga. However, like Sentinel, I too am skeptic to believe anything until we ascertain empirical roots on the subject.
My only other complaint about your theories is that they are heavily cross-linked. Ergo, they're dependent on one another. If one theory falls, then the next one falls, and the next one, and the next... kind of like dominoes.
On the other hand, the advantage of this is that your theories bear great consistency, so if one theory is correct... well, you get the idea.