The other protocol that might also help you is to supplement borax(Sodium Tetraborate). Borax is one of the few nutrients that will kill mycplasma and mycobacteria. And if it kills mycoplasma(a CWD bacteria) then it will probably kill Whipple bacteria. Another substance that also kills mycoplasma and fungus is Hydrogen Peroxide.
If you want to look at my full protocol against fungus and Candida -- it's here. My protocol will also kill and remove other pathogens that are always usually associated with candida -- like mycoplasma and parasites.