I am suffering from seviere headache and hyper acidity from last two years. Doctor said that it's migraine. What treatment should I take?

Headaches. If you have tried all over the counterpain medications, you might consider a magnesium supplement, then see your doctor. You might need a daily medication like topamax (topiramate) or Propranolol to keep the headaches away. You can also find out if your headaches are coming from tension, dehydration, lack of sleep/poor sleep, skipping meals, stress, sleep apnea/snoring, or chronic sinus problems.
Dyslipidemia. Iodine lack causes oxidative stress in gut. Thyroid needs iodine. Thyroid uses cholesterol to make hormones - if thyroid is low then body creates more temporary metabolities like lipoprotein a which is very painful since it causes damage to vessel wall with vascular inflammation - to relieve this use Niacin as neuro-htp available from biotics take 4 times a day for headache.