By lowering the pathogen load the Beck Protocol will indirectly help your body deal with parasites. I may be wrong but I don't think it is the most effective way.
I think you should try Dr. Sutters forum as they have dealt with problems similar to yours.
You should try Zymex 2 as it dissolves the worms before they know what hit them. That way their is less chance they will move to other areas of the body. Another one they recommend on the Sutter forum is Bare foots Dewormer.