You can take probiotics with parasite cleanse, according to Dr. Bailey, just like you can take them with Antibiotics .
As far as stomach pain is concerned, I had severe IBS until I started cleansing. I would be up at night in the bathroom literally screaming in pain. After the first round of parasite herbs, the IBS was gone, and it's never come back. Whatever it was (I passed a lot of Tapeworm and flukes, and some roundworms as well), it wasn't IBS. I love how they just make up names for things that are caused by parasites; fibromyalgia, lupus, chronic fatigue, IBS, Chrons disease...it goes on and on. So many people have been "cured" of these "diseases" when they got rid of the parasites.