I had low vit D throughout my second pregnancy too and lived with headaches right through. My migraines though were only in the first trimester and did get a little better on the Vit D.

Also, remember.. its bloody hard being pregnant when you have another kid. Its so much more tiring than the first time. Increasing your water to insane amounts will help also. Also, look at how your sleeping.. maybe its time to get a pregnancy pillow to put your body more inline when you sleep? If you are eating, try to look at some foods that may be making your headache worse.

Diet Headache Migraine: Foods to avoid

Top offenders:
Cheese (except cottage, farmer's, ricotta and cream), Alcohol (red wine is the worst. Watch out for flavourings (ie vanilla) which may contain alcohol), Caffeine (especially suddenly raising or lowering your intake), Chocolate, Aged and non-fresh meats and liver (ie cold cuts), -(also watch out for products with meat and hydrolyzed protein, such as gravy and soup mixes), Soy beans, Italian green beans, broad bean pods, MSG, Nuts (especially peanuts), Yeast (especially in homemade bread and sourdough), Sauerkraut (and other aged foods)
A big problem for migraine sufferers is food with tyramine, so there is now a page dedicated to cutting down on foods with tyramine.

Another theory is that tannins are diet headache migraine link. Find out what tannins are and where you find them.

Eat with caution:
Salad Dressing, Rennet tablets, Dried fruits (including raisins), Imitation crab, Licorice, Mushrooms, Snails, Salty foods, Rhubarb, Citrus fruits, Ripe avocado, Ripe banana, Yogurt and buttermilk, Fresh raspberries, Red plums, Onions, Worcestershire or teriyaki sauce. Wheat is a trigger for some as well.
Eat in moderation:
Everything!
Especially avoid sudden drastic changes in your diet, such as suddenly cutting out all caffeine or suddenly eating large amounts of peppermint. Whatever it may be, ease into it and eat a well balanced diet!

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Headache Fighting Foods:
In the world of diet-headache-migraine cures, the best advice is simply to eat a well balanced diet with plenty of fresh, non-processed foods. That includes a variety of grains, fruits and vegetables. But here are a few specific foods that you may want to introduce into your diet. These are believed by many to have the diet headache migraine connection, and may cut down on your pain:
Peppermint, Cayenne pepper, Ginger (more on ginger here), Fish and fish oil, Foods rich in calcium (such as spinach, broccoli and kale), Foods rich in magnesium, such as spinach (maybe Popeye was right! -read this article for more on the magnesium migraines connection), Oatmeal, Wheat, Garlic

I also wonder if taking a magnesium suppliment would help you?