Dear Jennifer,
Thanks for an interesting essay. I especially enjoyed your physical example of Gödel's theorem: "from within a GameBoy universe, the GameBoy cannot be entirely encoded and explained."
I also enjoyed your discussion of physical (thermodynamic) entropy and information (communication) entropy. ET Jaynes, the first to extensively link the two in 1957 reminds us of "...a persistent failure to distinguish between the information entropy, which is a property of any probability distribution, and the experimental entropy of thermodynamics, which is instead a property of a thermodynamic state... [Many] authors failure to distinguish between these entirely different things [leads to] proving nonsense theorems." Your observation that "there's no reason to quantify a quantity" seems original and worthwhile.
Also you mentioned that "anything you and I perceive... may be represented...". This establishes a link between perception and the physical world, while yet distinguishing between the two.
You ask, with Lee Smolin, "What is the substance of the world?" I hope you will enjoy reading my essay, where I make an attempt to answer this.
You make numerous mention of post-EPR, post-Aspect, but it is not really post-Aspect. It is post-Bell. Nothing in Aspect's experiment argues for non-locality. ALL non-locality arguments are based on Bell's inequality. If Bell made any mistake in his simplistic inequality, all of the following experiments do not prove, or even suggest, non-locality. Currently it's not fashionable to even suggest this, but it's good to keep in mind.
Michael Crichton had the right idea.
Best,
Edwin Eugene Klingman