Douglas Hofstadter is the go to, mainstream, "hey I recognize that name" authority, though it obviously should be noted that he is a cognitive scientist, not a biologist, neurologist, or nuero-biologist. So, you couldn't build a brain from reading Godel, Escher, and Bach. The only other material I intimately know that discusses the origin of consciousness is Carl Sagan's The Dragons of Eden, which, again, is mainstream and pop science. It's fun reading and enjoyable, but you can't build a brain from it. Someone else can probably suggest better sources for more study.

Of course, some components of these questions can be answered by reducing the question to find out more about what you're looking for.
What's the make up of an internal experience? What are its moving parts? How do you build it?
How are subjective experiences not physical processes? If they aren't physical, what are they?
Taboo "internal/subjective experiences." What are you left with to solve? What mechanics remain to be understood?

Since you've read through the quantum physics sequence, I'm sure you've been exposed to these ideas already. I'm not a neuroscientist or a cognitive scientist. I know very little about the brain that wasn't used for blunt symbolism in Neon Genesis or Xenogears. But I'd guess that, whatever mechanism(s) allows for consciousness, it's built using the matter available. No tricks or slight of hand.