I spoke with Dr. Cowden recently and he agreed with my concern about parasites being a big part of the chronic Lyme problem.
Dr. Cowden explained that it is important to start any Lyme killing protocol by attacking and eliminating the largest pathogens first and then moving down to bacteria then finally viruses and mold.
Many parasite detox products work for a short time but many parasites reproduce so quickly and in such large quantities that it is imperative to stay on a strong program for 8 weeks before starting the Lyme protocol. However if you are already on antibiotics or the Cowden protocol or some other killing protocol just dive in and do the parasite protocol at the same time.
Expect to feel worse before you feel better. Dr. Cowden recomend Nutramedix products to detox from the herxes (see Cowden protocol) but I have found Sarsaparilla (Smilax) to be very economical and effective. I take 4 daily and more if needed during a herx.
For parasites: Start 8 weeks prior to Lyme protocol: Food Grade DE (keep away from face) 1 tsp in 1 cup of water before breakfast (after 2 bites) and dinner 5 days on and 2 off; Artemesinin by Nutricology, 3 caps 2x day; Enula 50 drops twice a day for 8 weeks (all 5 days on 2 days off) then full moon cycle (2 days before, day of full moon and 2 days after forever!)