Dear Tim,
Thanks for your kind words, it is important for us to know that you appreciate our work - as we appreciate yours.
Of the four 'speculative suggestions' you mention in your nice essay, we have paid attention to three, obtaining some encouraging results. Entanglement is dealt with in several papers specifically for the two-particle case, fully in line with your point of view (see e.g. Physica E 42, 308 (2010) and Found. Phys. 41 (2011) 843-862). About the atomic line spectra, they turn out to be indeed due to sharp resonances, as you envision (some references are Found. Phys. 31, 1703 (2001) and Found. Phys. 39, 1240 (2009).) These two topics are dealt with at more length in Andrea's Ph D thesis.
As to your suggestion about particle diffraction, we fully agree with it. With J. Avendaño in Phys. Rev E 72, 066605 (2005) we present an exact calculation of the pattern of the random zero-point field diffracted by a single slit, which shows the presence of scars. In Physica E 42, 313 (2010) we make a very initial to attempt to see how particles are affected by the field diffracted by a double slit diffracted. It is interesting to note that the particles that are most diffracted are those that have a momentum equal to the momentum of the diffracted (and diffracting!) field mode. Unfortunately, due to both technical and personal reasons, this problem has not received due attention lately, but we hope to resume it in the near future.
Regarding your question about stochastic optics, Trevor Marshall and Emilio Santos, along with some younger colleagues, have continued to work on it, obtaining some interesting results, such as an explanation of some of the 'strictly quantum' phenomena of quantum optics as a consequence of entanglement with the zero-point field. We are sure that Emilio would be happy to give you more information.
All the best,
Luis, Ana and Andrea.