I had headaches as well. I cut out caffeine and that helped me somewhat. Caffeine also had a weird affect on my heart-- created some irregular heartbeats. I feel good now and only drink decaff coffee.
Hope your headaches go away soon. I went through stages of various physical things (only minor) my first month or two of being sober. I just kept in mind all that I had put my body through and pictured it healing itself... I think it takes awhile for everything to be back to "normal". I'm almost at 3 months and I still don't feel back to normal, although I do feel much, much better. Hang in there and try to relax as much as you can!!