Your headaches, as others have said, are a result of you being "on and off" of Atkins. Your body can't make up its mind about burning carbs or burning fat, and you're feeding the addiction by going off-plan. Give it a few good days of clean Induction, and you should be headache free. Tylenol or another pain reliever will help. Excedrin works best because of the caffiene, but you might want to try cutting that out.

Also, make sure you're eating something every 6 hours at least. Going without food for a long period of time will give me a headache.