As a long-time headache sufferer myself, I can sympathize with what you're going through. Here are my thoughts on the subject:

1. If you're eating enough, and still suffering, your body may be missing some nutrients. To the two already mentioned--calcium and potassium--I would add magnesium, and, especially, chromium (picolinate, take 400mg with each meal) to the list. Another thing that can help is glutamine, 2-5g per day, available at GNC.

2. Is your mouth dry all the time? You may be dehydrated. You have to drink LOTS of water with LC WOE, because the body needs lots of water to metabolize fat. I always keep a bottle of water on my nightstand, and when I awaken at night (I always do), I take a swig. If I'm unfortunate enough to sleep through the night, I'll often wake up with a dry mouth and a whanging headache.

3. You may need to ease into the low-carb thing instead of plunging in. Unless you're dangerously obese, you can dial down the carb intake gradually to reach the induction level (I know Dr. Atkins doesn't mention this in his book, but remember that most of his patients come to him with severe weight-related problems). Dialing down lets your body adjust to burning fat instead of carbs as a primary energy source. But make sure the carbs you consume are healthy ones; i.e., from fruits and vegetables or the occasional whole grain. No potatoes, pasta, or junk food. And NO CHEATING!

Good Luck!