Thyroid disease and now connective tissue disease as well, what's going on with my body?

Autoimmune condition. Hashimoto's and graves' are two thyroid diseases caused by the body's immune system attacking thyroid gland. In hashimoto's, the attack causes thyroid underfunction, while in graves', the attack causes overfunction. People with autoimmune thyroid disease are more prone to autoimmune connective tissue disease (lupus, rheumatoid arthritis, etc) when immune system attacks joints, skin, muscles, etc.