Hi thanks for asking question.
What is her thyroid report???Hyper or hypothyroidism???
So according to report correct thyroid problem.Like for 
hyperthyroidism propylthiouracil like drug and for hypothyroid 
levothyroxine can be given.
As hormonal fluctuation has role in triggering headache correct it.
When you have severe migraine attack for treating it take 
sumatriptan plus naproxen combination tablets.If ibuprofen like analgesic effective then first it should be tried.
If your migraine attack not resolved by above drug and attacks are more then 4 per month then prophylactic treatment can be started with amitryptillin or verapamil like drugs.
Meanwhile avoid triggering factors for headache like...
-Smoking
-alcohol
-bright light
-low sugar
-skipped meals
-sleep irregularity
-Loud noise 
-Stress etc.
Take enough sleep.
Massage and muscle relaxation exercise useful.
Coffe good in morning.
Basil leaves or oil useful herbal remedy as topical application.
Lavendar oil inhalation or topical application good one.
Meanwhile get your blood pressure measurement.If high treated.
Avoid 
hypoglycemia like triggering factor also.
I hope she will recover well.
If still your problems increasing then consult your er for CT or MRI scan.
Regards:
Dr.Parth