Richard - some excellent summaries in here, and (mostly) well connected with coherent insights. Nice job.
I did read all the way down the rabbit hole ...
Your comment that "To a hypothetical massless passenger, a photon is instantaneously everywhere" is not quite correct. The proper time depends on Lorentz frame of reference. For example, if our hypothetical massless passenger happens to be in the atom, the proper time of a photon is zero. If she happens to be traveling with the photon, then the proper time for whatever is going on in the atom appears to be zero. Lorentz Transformations are symmetric. [See Peres & Terno "Quantum Information and Relativity Theory" http://arxiv.org/abs/quant-ph/0212023v2 for an excellent description].
My favorite paragraph in your paper ... Well I have two:
"Wheeler and Feynman, in their time symmetric theory [22], theorized that no particle is emitted unless it is absorbed somewhere later in the universe. All electromagnetic field equations are invariant under time-reversal symmetry. Consequently, a wave can be considered going both forward in time from the point of emission (retarded wave) and backward in time from the point of absorption (its conjugate advanced wave)."
This [22] is (I think) where I got my original idea for subtime many years ago.
My second favorite paragraph:
2. "The process that selects the xt information encoded in pe waves is measurement. A recent experiment [29] showed that the measured spin state of an atom is correlated with the direction of the path of an emitted photon. Conversely, adjusting the orientation of the observed photon's polarization at the stop point alters the spin states of the atom at the start point, supposedly "after' the photon was emitted."
Thank you for finding this reference, this is terrific, and ties in well with how I conceptualize entanglement. However, note that in a reversible subtime scenario, the ordering of individual events (before, after) has no meaning.
This is discussed further in my paper: http://fqxi.org/community/forum/topic/1897