Inflammation can be caused by lots of things as can body aches and pains.

One thing I have been reading about lately is that hypothyroid may be related to fibromyalgia, the hormone one takes may not be enough or the way the body uses the hormone in pill form isn't the same as the way it naturally does, etc. I changed the maker of my thyroid pill, so I had fewer "inactive" ingredients and I have much less body pain. But I had to do that myself, my doctor didn't have the time/inclination to look into what is supposed to be the "same" hormone, no matter who makes it. But there's lactose in Synthroid, for example, and that was giving me all sorts of bowel problems! :-) as I'm lactose sensitive.

I would have your doctor do a full physical and I would look at any of your medications and see exactly what is in them and what side effects they have, etc. and look at your diet and exercise routines and your whole lifestyle and play around with that, get as "healthy" as you can figure out how, for yourself. I'm glad you know it hurts and that it isn't "in your head" and that you're asking questions and looking for your own answers. I don't throw my doctor out with the bath water but I sure don't lean on him exclusively. He's just a guide, it's my life/body.