Hi Driven!
Welcome to our community. I"m so glad you found us.
If you haven't yet, it would be helpful for you to start with reading through the thread at the top of the forum titled,"New to Lyme?...Start here!!", as it is packed full of important information, symptom lists, helpful links and pdf's, how to detox when one has these infections, information on probiotics and much more. And this is another good list of possible detoxing routines:
www.tiredoflyme.com/detox-methods.html You definitely need to be detoxing, as this will likely help ease your symptoms. It sounds like you may be herxing.
Yes, you should be using a probiotic, as the herbs will kill the bad bacteria off in your digestive system, and you need to replace them with good bacteria to keep the levels of the bad bacteria down. Otherwise, more bad bacteria is allowed to proliferate in the intestines.
There are many types of probiotics that can be used. You want to find one that seems to work best for you. I prefer kefir (homemade), but others have used VSL3, Florestor, and others. Basically, you want the highest number of strains of bacteria that you can afford, from a good quality brand though.
I'm not sure if adding Oil of oregano would be a good idea right now, if those are the symptoms that have increased since starting the protocol. You would do best to wait on adding that until after you get the herxing back under control, as oil of oregano can really pack a punch for some people.