One comment on your serial (single threaded) vs parallel (multi-threaded) computing. Algorithms can be multi-threaded and look out for quantum computing in the relative future.
Yes, a physical part of you makes the decisions, but it doesn't happen consciously. Training and learning make a difference which is why the belief that free will is an illusion doesn't mean that we shouldn't try. Instead it should make us less arrogant and more compassionate because we didn't choose our atoms and neither did anyone else. I like Sam's concept of "living an examined life", it fits perfectly with my mindfulness concept of being present.