Ditto IrishHeart. My chronic C started to go after about 4 months once I began thyroid medication for hypothyroidism. At 11 months gluten-free, and 9 months on thyroid meds, it is pretty much better. I found patience was really helpful... And that is all that was helpful. Lol. I hope it is fixed for you soon.
Gluten could have snuck back into your diet somewhere. I did that a few months ago - I nibbled on some fries that had gluten every few days and felt poorly for a month or so. It was mainly intestinal and headaches that came back for me.
I think the symptoms like pain and fatigue are harder to get rid of and tend to keep cropping up for months, or even years, after going gluten-free. When I had been gluten-free for three months, I had a bad autoimmune flare-up of some sort with symptoms that included deep fatigue, arthralgias that were affecting my everyday movements, and increased hairloss. I though something else must be wrong with me but my doctors seem to think it is still my body healing from years of gluten caused injury. Apparently it can take a loooong time to get rid of all symptoms for some people.
It could also be your hypothyroidism acting up, or even healing on gluten, which could alter your thyroid medication needs.
It could be other food sensitivities too. dairy is a common offender for many celiacs in the first few months. It is possible something else is not agreeing with you. I have discovered something in my Vegan protein powder that makes me react with bloat and stomach pain but it appears to be gluten-free, and I don't eat enough processed foods to pin point which ingredient was doing it to me. A food journal with symptoms might help you figure out which foods are causing problems or if gluten is in your diet.