That's quite the pontification. Alas, you're preaching to the converted. I subscribe to philosophical naturalism and to cognitive science, and I argued for the same blind brain theory of the "illusion" consciousness in "The Limbo from the Labyrinth: Consciousness and the Brain" (first link). I also wrote an epistemological series on how each concept and thus every instance of understanding simplifies the subject matter.
But that doesn't mean that cognitive science entails eliminativism about qualia. We can't even say that something's illusory without presupposing the reality of qualia. An illusion isn't just a conflict between mind and world, or between neurons, since that would be a physical matter of cause and effect. Instead, an illusion is how one thing seems to be something else. And it's that seeming that's qualitative, and thus that's not found in the neurons. The neurons that correlate with the taste of broccoli don't themselves taste like broccoli, nor do the neurons that support the seeing of an apple look like an apple.
Consciousness emerges from the brain, as I say in all my articles on consciousness. Consciousness is a neural trick or illusion, but illusions are real enough. Go to a magic show and you'll see tricks that generate the illusion that magic is occurring. That illusion exists not in the physicality of the magician's sleight-of-hand maneuvers, but in the audience's thoughts and perceptions. It looks to the audience members as if magic has occurred whereas in the external world there's no magic.
To speak of an "illusion" is just to grant the existence of qualia, and that's all I mean by a "ghostly" self. I don't mean anything supernatural, but a mind that emerges from the brain, an illusory/ghostly self that suffers the existential condition of feeling alienated (because of the brain's relative blindness to its operations, etc).
