@DonkeyDude Your wife's hypothesis about having run so long on stress hormones jibes with my experience as an explanation for your fatigue.
After a decades of running on adrenalin/cortisol to feel "normal" before discovering Peat and experimenting with exogenous thyroid supplementation, I seem to recall that there were many times when eating a carbohydrate-rich diet or taking supplements to decrease/oppose adrenalin or cortisol, I experienced paradoxical results in the first 3 to 24 months similar to what you describe.
Even after normalizing thyroid (at least in the blood), I think I continued to behaviorally/psychologically "crave" stress to feel the endogenous stress hormones I was unfortunately so accustomed to: sleep deprivation, HIIT, anger, provoking conflict, etc.
Does anyone know if there's any literature or if Ray wrote anything regarding how long it takes to re-establish thyroid homeostasis in tissue -- across the many different types of tissue in the body -- following early responses (as expected) to thyroid supplementation (e.g. normal serum levels in thyroid-panel blood tests, normal body temperature, normal-range speedy Achilles tendon reflect)?
I once asked a very well-published senior endocrinologist (indirectly about Ray's critiques of endos relying too much on blood tests) whether he thought blood tests implied normal thyroid action in the tissue. His response was entirely sympathetic to Ray and other's critiques of over-reliance on blood tests when assessing a person's thyroid status. He went on to say that, because biopsies of human tissue are invasive/impractical/expensive -- and maybe also because the available techniques to analyze what healthy thyroid action looks like in tissues, e.g., leading to ample ATP production (I'm not sure about how good the existing lab techniques are), we know almost nothing about thyroid action in the tissue for a typical patient that endos see!
I'd be curious to hear other thoughts about reliable tests (we probably already know a lot of the common symptom profiles we can notice ourselves) to assess thyroid saturation/action and efficiency of mitochondria and ATP production. Given unlimited money, willingness to be biopsied, and access to the best university labs (not just run-of-the-mill tests offered by Labcorp, etc.)...how reliably might one measure thyroid levels in the tissue?
I suspect it's possible to have normal-to-high free T3, very good body temperature, and still suffer from metabolic problems (insufficient ATP or inflammation) in one's brain tissue (or elsewhere).
In my experience, homeostasis (of a much improved kind) eventually came after multiple years of Peat-inspired diet and thyroid supplementation. But the improvements were not in lock-step. The most frustrating and noticeable paradoxical situation was just as you described: achieving high body temperature with NDT or T3 and having brain fog, malaise, incapacitating fatigue (in the first month or so). I think it was the result of being an adrenalin/cortisol "addict". Brain fog and psychological tone lifted noticeably after 2 or 3 months of thyroid meds for me. But other improvements took longer.
I also don't think re-establishing homeostasis after beginning thyroid meds is typically a path of "steady", one-way (i.e., monotonic increasing) improvement. There should be improvements to justify continuing with the experiment, and it sounds like there were! I would expect that there will also be frustrating and unexpected (hopefully temporary) setbacks -- like waves of fatigue because your adrenalin/cortisol is much lower than you're used to.