Before getting into a full discussion, please post your Reverse T3 result, and identify when it was done. Also, please post your Vitamin D and B12 result. How long ago was the AM cortisol test done, and when you say it was high, does that mean it was over the range limit or just high in the range? Have you ever tested for ferritin?
Obviously your test results are consistent with being hypothyroid. Your Free T4 is higher than necessary, but your Free T3 is too low in the range, which is quite common when taking only T4 med. With your Free T3 to Reverse T3 ratio, you really do need to reduce your RT3 level and increase the FT3 level; however, in view of the reactions to NDT and T3 in the past (which can be associated with cortisol and/or ferritin), I suggest that you hold off on that until you find out about your current cortisol and ferritin levels.
High RT3 has been postulated to be due to a broad spectrum of abnormalities such as: leptin resistance: inflammation; dieting; nutrient deficiencies such as low iron, selenium, zinc, chromium, vitamin B6 and B12, vitamin D and iodine; low testosterone; low human growth hormone; insulin dependent diabetes; pain; stress; environmental toxins; free radical load; hemorrhagic shock;, liver disease' kidney disease; severe or systemic illness; severe injury' surgery; and toxic metal exposure. Clearly the number of variables makes it difficult to test enough to pin down potential cause(s); however, note that low Vitamin D is included.
So, one suggestion is to increase your Vitamin D level. I can't understand why you would have a reaction to D supplementation like described. In the following study it concluded that low D is a possible cause for IBD. So somehow you need to raise your D level to about 50. I expect that it will take about 3000-4000 IU daily of D3. You can also take more magnesium and Vitamin C to offset any adverse effect.
I also think that the Free T3 level you do have is likely not adequately getting into cells of your body due to the high ferritin level and high cortisol (if you still are high). This would further add to your hypo condition.
Unless you are supplementing with iron, I suggest that you should be tested for ferritin again and a full iron test panel (serum iron, TIBC, and % saturation). Along with that I suggest that you get new tests for cortisol. I suggest a morning serum cortisol, and a diurnal saliva cortisol panel of 4 tests. It may be that your sleep issues are related to cortisol level. Once you have these test results it will help greatly to determine further action.
I also have a side question that I have sent to you in a PM. Please click on your name and then from your personal page, click on messages.