Hi Tim,
Nice essay. I will have to read more about your Theory of Linear Structures at some point. It seems to have some similarity to what Kevin Knuth has done with posets, and with some of the things I'm doing right now with information orders on domains (building on the domain work of Keye Martin -- not sure if you are familiar with any of it).
I think you also hit on something interesting in regard to this idea of counting and how it relates to a physical ontology. One could argue that, even if the universe is entirely continuous, our ability to measure it to arbitrary accuracy is necessarily discrete and thus the integers match up well with that discreteness (which interestingly links back to a previous FQXi essay contest). Just a thought.
Anyway, I nevertheless must admit that I didn't find your argument convincing in general. It seems to miss some subtleties. Perhaps these subtleties are addressed in your larger work on the topic, however. For instance, I disagree with you on a key point: I do think that how different branches of mathematics relate to one another, has a direct bearing on how mathematics relates to the physical universe. How could it not? If you are familiar with category theory or topos theory, think about how such theories describe both mathematics and physics and their inter-relationships.
I had a few minor quibbles as well. In the example you gave of a universe describable entirely via fluid mechanics and dynamics, you would still be faced with the distinction of "something" versus "nothing" which maps quite naturally to 1 and 0 respectively. Integers are an elementary extrapolation from there.
I also am not particularly awed by the fact that results in semi-stable elliptical curves were used to prove Fermat's Last Theorem. While I am not deeply familiar with the details of Wiles' proof, in some sense both elliptic curves and Fermat's Last Theorem deal, on some level, with polynomials. Certainly the connection is not obvious, but neither is it all that shocking, at least to me.
Cheers,
Ian