Dear Christopher,
I find your idea about an axiom of measurement very interesting. Allow me to suggest two ways to formalize your idea a little more:
1. Reformulation you axiom or measurement as a standard set theoretic axiom schema:
Let x be any physical or mathematical object
Let phi_i(x) be a formula which expresses a particular formulation of the axiom of measurement e.g. "x is diffraction limited"
Let S be the set of all objects which satisfy what might be called a "measurement condition" (i.e. they are empirically measurable).
Then, it seems to me, your idea can be expressed in the form of a simple axiom schema:
[math]\forall x (\phi_i(x) \Leftrightarrow x \in S)[/math]
Notice that purely mathematical objects satisfy neither the left nor the right side.
2. Specifying that urelements are allowed in the set theory and correspond to physical objects
One issue you may want to consider is that standard set theory is built purely out of sets. Your idea would require the pursuit of one of the variants of set theory which are built out of atoms or urelements (like ZFA), so that when x is a physical object, it can be represented as such.
I hope you found my feedback useful.
Best wishes,
Armin