Sounds like a puzzle! Thyroid can have a wide variety of symptoms, so it could be that even if he doesn't have the typical ones. Definitely sounds like some low grade, multi-symptom "off". How's that for a diagnosis
FWIW I have been feeding raw for 10 yrs, and I have had several dogs that didn't do well on the commercial raw mixes. And some that did fine, of course. I always blamed the veggies, but since I only use it as a supplement of special occasion, like after a dental, I never really investigated.
If things don't improve, I would guess more tests are the next thing.