I haven't specifically suffered from headaches, but the repairing our body needs to do in order to function more efficiently has many side affects.
I started keeping a journal where I charted my mood and physical ailments. When you keep a record of how you are feeling, at what time and under what circumstance it is interesting to see how things coincide. Our bodies tell a clear story if we listen to them. One of the best things I have ever done was taking a step back and listening to my body