I am left to make one single note: how you describe your experience with academia, as kind of latter-day autistic positivists, is different from mine. In physics, my teachers were adamant that we notice the holes in the theories we learn about, already in the Newtonian, and the problems of interpretation. (Coming to the current stage, one of my teachers made the point that the greatest shortcoming is not QM interpetation, QFT renormalisation or nonlocality; but something affecting even would-be quantum gravity theories, the lack of time assymmetry/causality.) *Lunatic*, n. One whose delusions are out of fashion.
Or not: Thank you for describing your experiences, which are not only interesting to read, but show that it matters a good deal HOW the work of science is conducted--that is, the social and emotional atmosphere. The Fates are kind.