The questions of consciousness which you raise are the subject of Penrose's two books Emporer's New Mind and Shadows of the Mind. I strongly recommend them both.
Francis Crick has taken the materialist view in his book The Astonishing Hypothesis. I read someone bemoaning that to really explore his theory, we'd need human subjects. Kind of a knock-out gene approach on grey matter.
You might be interested in the reasons Penrose gives why consciousness cannot be simulated (automated) - he is not a computationalist, and thus not in favor with A.I. people (LOL!)
But all of this research notwithstanding, there is still the unconscious which is not addressed.
My two cents is that the spiritual realm is separate from the natural realm and that the brain acts as a receiver for the spiritual realm as well as performing functions for the physical body.
Some researchers in near death experiences share this view and are building a body of evidence. Because it smacks of the mystic, I'm not expecting it to be embraced by conventional science. For one thing, it cannot be falsified.