I had hip pain that resolved after being treated for a vitamin D deficiency. I was diagnosed with Hashimotos at the time as well, and continue to have issues keeping Vit D and B12 levels within range.
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I was diagnosed hypo in 2008. After 2 md's and 2 endo's telling me that my thyroid was dying and levothyroxine dose would increase over time and that would be the only thing I could expect to help with the many symptoms that I was experiencing, I got busy reading. For me, natural desiccated thyroid hormone (Armour) and an elimination diet (The "Plan" by Lyn Genet) gave me the most relief. You must educate yourself on autoimmune disease in general and reading about the experience of others with hashimotos is also very helpful. I am on a gluten free, low sugar and minimal dairy diet, take B12 and D3/K2 and selenium supplements, among others and exercise as much as I can tolerate. Some resources that I have found helpful: Chris Kresser, Izabella Wentz, Amy Meyer, Sarah Zeilsdorf to name a few and there are soooo many. Read, read, read…..
Hashimotos is miserable but manageable and possibly controllable. If you don't manage it you may find yourself with additional autoimmune disorders. None of them are pleasant…
I wish you good luck and success on your journey. Remember that YOU are the key to taking back your health and you will be ok. Don't give up.