good report, and there are some things i would do after having read it.
i would avoid doing things that stress the hive. if we follow the most likely line of thought at the moment, and the culprit is opportunistic, we can reduce our chances of having take hold in our hives by not giving it an opening.
if i were to lose a hive, i would not reuse the supers/frames, or at least the foundation. if i were to re-use the boxes and frames, i would certainly use proven methods for removing fungus and bacteria. (understanding that these are not fool proof)
if i found a hive severely compromised, i would not combine it with another hive without knowing why the 1st was in trouble.
and most of all....keep up with the research!!!