I am sorry to hear of your difficulties. Poor control of the thyroid hormone, especially low levels as in hypothyroidism definitely affects the menstrual cycle. And low thyroid hormone can also cause fatigue, muscle and bone pain, weight gain, constipation, feeling cold, slowed and depressed. It is also possible to have thyroid cysts without affecting the function of the thyroid, and if your thyroid function is normal, then the cysts are not responsible for the menstrual irregularities or joint pain. Cysts are sometimes treated with thyroid hormone to prevent them from enlarging. You may need to call the doctor managing your thyroid to clarify your thyroid function. When menses does occur it is usually associated with a low level of the cyclic hormones, both estrogen and progesterone. The change in the hormone levels can trigger migraines in women who are migraine prone. Many women know they are about to start their menses because a migraine started. Ovarian volume is often asymmetrical, and shouldn t cause you concern. Sometimes oral contraceptives are prescribed to women to regulate their cycle and if the placebo or blank pills are skipped over (continuous use) periods and the menstrual migraine can be avoided. Pills are not usually used in women who have migraine with aura….pre migraine visual changes, or sensations. There are several meds to treat acute migraines, and several others to prevent migraines from starting at all (chronic suppression). I hope that a neurologist or good gynecologist can advise you and that you feel better soon.