This all sounds pretty much consistent with my guesses about what was happening. In particular, I'm predisposed to agree with your idea that sleep is a bunch of different processes that are normally well-coordinated. I hypothesize that the combination of my Chronic Fatigue Syndrome and the doses of modafinil disrupted that coordination, resulting in my experience of being awake and asleep at the same time.

Of course, just because we both came up with similar hypotheses doesn't mean we're right, but I'll take it as a tentative working theory for now.