In a sense the hardware, software analogy is only true at the extremes, that is, basic brain architecture is hardware, and basic structural mythology is software..

I'm not sure what you mean by "structural mythology."  Could you please point me to a definition?

Sapolsky at Stanford seems to get "the basic sociological aspects of the psychology-effect in the pattern of learning which modifies the physical driving."  He's been studying the Forest Troop and has come-up with some interesting findings.

...but the living reality, as you say, is the messy middle when everything modifies everything.

This reminds me of the John Nash response when someone asked him, after his paranoid schizophrenia was overcome, why a man who had accomplished so much intellectually got to a point where he thought "there was an organization chasing him, in which all men wore red ties."  [From the link]  His response was, "That idea came to me in the same way as my previous ideas."

Heh.  Indeed they do.

She believed in nothing; only her skepticism kept her from being an atheist. -- Jean-Paul Sartre