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.
Adding a penny to your two ... Penrose seems to be that very rare scientist who combines extremely high intelligence, feel (he writes of Einstein's "instinct") and the courage to "go public" with what he doesn't know, and to take the latter as a challenge to discovery. There is without a doubt an intangible realm that plays an integral and highly meaningful part in physical reality. There are tons of evidence here, very little of which is acceptable to science, which I suppose should not be surprising given science's insistance upon tangibility. While the scientific and very human habit has been to insist that we do know, Penrose thinks and thinks and circles and circles and will not give in to that very great temptation, the Materialist temptation.
If the intangible is real, there would simply have to be some operative interface between it and the brain, and to look for it makes all kinds of scientific sense, to me at least.
My take is also that whether or not Penrose is aware of it, and I think he probably is, he leaves open the scientific door to mysticism, which he seems to believe and I would agree can be approached from the scientific side. NDE, and other heretofore "verboten" phenomena, may thus become legitimate subjects of scientific study. I believe they will, with time. All IMHO, Alamo-Girl.