It seems to me that you are trying to build some kind of philosophical system centered around anthropology, morality and politics. However, any system is only as good as its epistemology. And to be honest, I find epistemology of this "corpus" to be weak and self-contradictory.
You constantly emphasize rationality, that everything has to be logically sound, or it falls. You even have "AXIOM 3: RATIONALITY TAKES PRECEDENCE OVER ALL OTHER VALUES." But, then you present the very definition of axioms as: "AXIOMS. Chosen starting points. Not derived. Not proven. Selected. The reader can reject them. If the reader rejects them, the derivation does not apply." But even though axioms are not something to be proven, they still need to be justified (usually this is done by direct personal observation). If something is not justified, then it is not rational to accept it in the first place. Therefore, framework which fully embraces rationality can not work if it also embraces arbitrary starting points. To be clear, there is nothing wrong with hypothetical thought experiment "if those things are true, then those things follow". But if I understand correctly, your goal is to prove something real, something that will help human flourishing, not just that hypothetically, if those axioms are true, certain conclusions follows. To summarize, without further justification, there is no rational reason to accept any of those axioms, and because your system is based on accepting only rational things, it is self-defeating.
Then, you have "AXIOM 5: UNCERTAINTY IS PERMANENT. You cannot know anything with absolute certainty. You cannot rule out most things. You must act under uncertainty." But this flatly contradicts another part: "THE FOUR CATEGORIES OF KNOWLEDGE ... 1. BEDROCK Irrefutable facts derivable from physical constants, verified historical events, logical axioms, mathematical proofs. Examples: thermodynamic laws, verified historical dates, logical tautologies. Confidence level: High. These can be stated with certainty."
Next there is claim that you removed "The free world must be defended." and "The cost is acceptable." from axioms, because they are conclusions. But this further blurs whole concept of divison of axioms and conclusions. If your axioms are simply chosen, there was no need to remove those statements. But if you consider statement that can be derived from something else to be conclusion and not axiom, then you have to remove at least four other axioms: "AXIOM 1: SUBJUGATION IS WRONG." "AXIOM 2: THE SPECIES IS THE TRIBE. ... No subgroup - race, religion, nationality, ethnicity - has priority over the species." "AXIOM 4: HUMANISM TAKES PRECEDENCE OVER NON-SUBJUGATION." "AXIOM 6: THE INDIVIDUAL IS THE UNIT OF MORAL WORTH." Because those are all moral claims, and every moral claim can be derived within some broader moral framework.
"AXIOM 6A: DEFAULT AGNOSTICISM ABOUT SUPERNATURAL CLAIMS." is redundant, as from rational inquiry follows, that we should start with agnosticism about any claim.
It is my opinion that osdevers have the extreme technical skills required to take on a project like this. ... But who on earth do you think is in charge of DOING SOMETHING ABOUT THAT? ie ENGINEERING AN OVERRIDE. The answer is - no-one. Just a whole bunch of bystanders who assume that someone super-smart is "on the job". And the solution is in the question. We need ENGINEERS. For a field that doesn't exist. Software engineers are the most obvious match, with our brains basically being software.
No. You are looking for philosophers. Philosophers are specifically trained in critical thinking and proper reasoning, and they are working on exact questions you are trying to dissect. Whole purpose of morality is to find how things ought to be, and that includes how we should act about our inherited - as you call them "chimpanzees" - instincts. I personally like philosophy very much, which is also reason why I take some look at your documents. But taking it all together, because "The corpus derives from first principles.", I do not see reason to continue further, as even the very starting points are not something to be accepted even within the system itself.