parasites can cause headaches, but would be really hard to say if you have them in the brain area. I knew I had them when I could actually feel one creeping around up there, then I got these unbelieveable pains in my head. I never get headaches so this was a signal that something was really wrong.
In order for your para cleanse to be effective you would need to take more that one dose per day. After 3 weeks, it would be good to take a break at least for a week. If not, parasites become acclumated to the herbs, rendering the herbs useless.