Good points. Seen in such light, self as mental approximation of environment and brain activity itself, no matter its complexity, is obviously the primary "tool."
As for brain, a funny anecdote is that even Aristotle considered it to be merely a radiator to keep heart from overheating. With that being said, I, too, assume naturalism here. I just differentiate between the observed (or known) "brain-constructed-self" and the observer.
Of course, no one can say for sure what's the deal with consciousness (awareness is pretty well understood), but if it is a brain epiphenomenon, question arises, how can trillions of individual unique brains (at least all mammals and birds, if we go strictly with what was demonstrated) produce a phenomenon that is identical to a T, as consciousness is without any properties whatsoever (all properties are always that which is observed).