Have you had your antibodies checked? I ask because
ovarian cysts, acid reflux, leg cramping, chest pain, eye pain, could also be caused by Hashimoto's antibodies. Hashimoto's causes hypothyroidism, and if you haven't had your TGAb and Anti-TPO blood work, I suggest you get it, along with a thyroid ultrasound.
The treatment for Hashimoto's, just like hypothyroidism, is hormone replacement like the brand you're taking, but there are many brands and formulas.