Hypothyroidism is a cause of TMJ dysfunction. Magnesium deficiency can also cause or worsen TMJ dysfunction and is also a well noted cause of migranes. Hypothyroidism can lead to low or deficient magnesium levels.
What is TMD , is that TMJ? If so I hear it can be painful & cause all sorts of headaches & jaw pain, especially when eating.
My throat never had pain due to my toxic goiter & it was huge at the time, it was the only reason I discovered it was my thyroid.
I don't know what you mean by autoimmune thyroid? Did he mean you have hyper/hypo/hashi's? Did he do any blood work.
I don't what you mean by inflammation in the brain due to thyroid.
Sorry...Wish I could help you more, but MANY here will jump in, they may just be in bed for now. But continue to check tomorrow, they will reply.