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He did know what he was doing, subconsciously. That's the art of the guitar solo, though. It's an accumulation of subconcious efforts. That is why you solo over the chords. If you want to follow theory 100% blatantly, don't solo at all. To do a prewritten solo destroys the spontaneous invention that makes a solo work. Hendrix, again, is a great example of this. There's a reason why his band would continue playing chords, and he'd go off into lala land playing randomly whatever worked for the time, and moment. The expression of spontaneous feeling.
Nah, his band was just a drummer, bass player, and him, so more just the bassline. I know a lot of people don't like Omar, but some of his solos during the songs he just goes to whatever note at random and goes with it. That gives his solos sort of an atonal and spontaneous feel. With Hendrix type solos I think you have to be a little conscious as to where your fingers are but once you know the scales and modes it's much easier to improvise and play around.