Hi there! Congratulations on sticking with it through a rough patch. I am on Atkins, and am now at my goal weight! I can tell you a bit about my experience, especially with headaches.
I used to be a chronic migraine sufferer. One way to combat the headaches on Atkins is to bend Dr. Atkins' rules a bit. You see, Dr. Atkins recommends that you banish caffiene from your diet, along with all of the other bad things. This is the one piece of advice that I haven't heeded, and here's why:
All of the "miracle drugs" on the market today that have a "special enhancing ingredient" are simply run-of-the-mill pain killers with caffiene. See, caffiene has a specific physiological effect: it helps to slightly constrict the blood vessles in your brain, thus helping to ease the pain of a vascular headache.
When you eliminate caffiene from your diet, you may find yourself getting headaches. I did. I find that a cup of coffee with cream and Splenda in the morning will head this off at the pass. In addition, there is a good deal of new research out there indicating that caffiene consumption (in moderation, of course) can be especially beneficial for the mental health of women as they age.
Like everything, the jury is still out. However, I find that bending the caffiene rule leaves me feeling energized and headache free.
Annie