hi kevin,
sounds like you've got a wide variety of ideas to follow up on, i'd also suggest testing for food allergies. while you eat clean/vegetatian, grains, fruits and nuts may also cause you grief - perhaps something has come into season? I was allergic to stone fruits, nuts, pineapple and oranges. go figure.
its probably a good reminder to everyone to get themselves a health check up particularly if something is niggling
