The headaches are probably the caffeine withdrawl. you're not having as much and are suffering for it You can cut out the caffeine completely which in a few days they'll ease off. Or just decrease the amount you have and in a few days your body will adjust to the new level. But yeah the head aches can be nasty!!!
On strict atkins you aren't supposed to have caffeine so people switch to decaf, herbal or green tea, but it only affects some people's weight loss. Determine for yourself. But that's just my opinion. ttyl!