Regarding Elite and it's representation in the game files, that's why I don't think a Disciplined unit can be "upgraded" to Elite with a Military Academy. Units can be both Elite and Disciplined (Jannisaries), they can also be Elite and Uncontrolled (Lancers). According to the official strategy guide though, non-Elite and non-Disciplined units count as half units when routing near a Disciplined unit for morale purposes, so there is some relation.
I'm not really sure how the upgrade works wrt Uncontrolled/Normal/Disciplined, I've never really paid too much attention to it. My guess is that Uncontrolled units become Normal, Normal units become Disciplined, and Disciplined units are not changed. Is it possible to see a unit's discipline state from the battlefield GUI or log files?
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