I keep thinking about this problem. And I keep asking myself the same question: what changed?

If I read your initial post correctly, it seems as though the engine did start right up in it original "crate" form. Yes? If that is true, then get it back to that state and start changing things one at a time, testing after each. In my mind, that's the best way to identify the culprit. Right now, I think you have too many variables, but that's just my opinion.