I'm hypo so i can't really say i know much about how to manage hyper. Buttt, i would suggest that to prevent any further damage, you take on an anti-inflammatory diet (i've used paleo autoimmune ,but that's because i have hashimoto's thyroiditis, the autoimmune disease and i need to keep down inflammation).
I would start up on vitamin D right away, because mine was very low too and i never supplemented with it and a few months later, i developed the autoimmune disease. Vitamin D plays a huge role in your immune system, and a lack of it can actually contribute to the triggering of autoimmune diseases, especially if your gut is not healthy.
I'm still suffering from extreme fatigue, so i'm sorry i cant give you any advice for that, but i do wish you all the best and hope that your recovery is quicker than mine has been so far!