Dear Odessa,
Thanks for showing an interest in this - yes, I agree, the next step in this project would be to find a formal system that naturally includes urelements of the sort needed. It's interesting, my main thought when writing the essay was how to carefully define the nature of truth in an experimental context, whereas most people's response has been like yours, worried more about the formal system.
In any case, it is a bit outside of my area of expertise but when I return to this project I feel that there are two major pieces:
1) Determine which variant of set theory is appropriate and carefully formulate it.
2) Use language within the formal system to carefully define the axiom of measurement. This would likely be a recursive sort of definition, since the truth in experiments only comes from the truth in earlier experiments. The choice of set theory would have to include such axioms.
After that, maybe try to fit a few physical theories (GR, QFT, etc) into this framework to illustrate how it can be used in practice to formalize these systems. Beginning with axiomatic field theory might be natural, since that philosophy is rather built-in already.
Again, thanks for you interest and your comments.