The Thing That Most Perplexes Me about Naturalism

I once had a conversation with my wife where I was trying to explain to her one of the main reasons I find the naturalistic worldview to be untenable. She was not understanding what I was trying to communicate so I drew a box and had an arrow pointing toward the box and an arrow pointing away from the box. I labled the box "human brain" and the arrows I labled input and out put. Clearly my point has been made right?

However, my wife was still not understanding, so being the genius that I am I drew the exact same picture, only larger, and began to pound the eraser of the pencil on the picture. Thankfully despite my inept communication attempts, my wife's actual brilliance kicked in and she understood my point. My wife looked at me and said something along the lines of "so your saying conscience thought always comes after the brain has done its thing not before."

This is one of the most perplexing things I find about the naturalistic worldview. Our brains are only physical, and without a soul, our thinking can only be the operation of chemical and electrical reactions. It would follow, then, that no one believes what they believe based on rational thought. Rather people have to believe what they believe because their brain just happened to fire a certain way.

Rational reflection would be impossible because by the time we have thought "I wonder if this is true" our brains have already undergone the chemical electrical process that produced that thought. Maybe I am missing something, but for now, I will file this under things that make me go ummm.