I hope it helps someone too. Nice post.
I still see nothing that explains how/why cam timing could not cause the problem. I too have a lot of experience with tuning. That doesn't make me an expert though. I agree with most of what you've posted, but it is only an introduction with many loopholes for contradiction of the implied theory. That's the nature of the beast though. Hence there is still no perfect model for engine combustion.
Back on topic.
Poor tune = burnt up engine. Tuning is tricky, but it isn't voodoo. It seems that way though because the consequences for screwing up can be very expensive unfortunately. If you'd like some pointers for tuning, let me know. I don't know how far you want to get off topic.