Much like above posters, I can't see how you could dispute "Something thinks therefore something is". Since the "I" is not specified in the original text (but it's nearing 10 years that I read a translation of it so take this with a grain of salt) I would say the substitution makes sense. At the very least, it is the meaning that everyone I ever discussed with was using. (I believe the "I" was merely a self referential concept, maybe like "this" in some OOP languages refers to the specific instance of the object in question).

As for the thermodynamics in Matrix, I faintly recall something about a fusion reactor working somewhere, but that may have been to power Zion, not the Matrix. I agree it is a colossal blunder in the whole series (and anyway, it would have been better if Reloaded and Revolutions were never made, Reloaded especially was unforgivably bad).