Hello Bonnie, i am sorry to hear you are in so much pain and I don't know if I am the right person to advice you, so I tell you my experience.
I am just passed the year mark and still having very very bad spells. In the past when things were really bad for a longtime I asked myself the same question as you did right  now, and for me to get an answer to that question I did stopped my protocol not the diet for a couple of days to 1 week and yes I did see changes in my level of pain, but I also knew that it  would not bring me the healing that I am so hoping for so I started it again.
For me it was a right decision because I did get an answer to the  question and it did give me more peace also I could give  Dr. Matia more information about my reaction to the herbs. Dear Bonnie it is not the end of the world to stop the herbs for a short while and see if there is a change painwise as long as you are doing the diet. If there is no change your question is answered as well.  Both yourself and Dr. matia are getting more information if all of this is a reaction to the herbs or not, but ultimately we know we have to start the full protocol again to achieve more healing but maybe with a change in the combo.Have you you asked Dr. Matia what she thinks is best?
I truly hear you Bonnie people in my family were saying the same thing so in the end I did try just for a couple of days and it did give me more peace to know that I was reacting to my combo or even to a little bit to much die off at that time.
I hope you can make the decission that is best for you and that you feel calm with it. Sending you a lot of hugs and healing wishes from overseas.

Hello Bonnie! I too went off my protocol for about a month just over a year ago! It was something I needed to do for many different reasons1)medical testing 2)wanted to prove to my Dr. that what I was taking was not the cause of any of my down right scary medical issues 3)and  in hindsight to prove to myself that this was the right path. Dr. B wasn't overly excited about my decision for fear I would regress too much during this time, but in the end she understood why it was so important to me. I didn't stop the diet either, just the supplements. It was really rough, I felt pain levels increase pretty quickly and symptoms started to return! I kept in close contact with Dr. B in the process, which she said was very helpful to know that certain things were definitely improving on the protocol. We all have our reasons for wanting/needing to take a break sometimes, it is alright to feel discouraged and scared! Bonnie, my dear, we are only human! Do what is best for you! If you do decide to take a short hiatus, say for 2-4 weeks, listen it isn't the end of the world! Who knows it may help guide Dr. B in a different direction with your treatment! Don't get me wrong, going off the protocol isn't the right thing to do for everyone, but because of other serious medical issues I was dealing with, it really was my only option at the time. In the end I am still here, and it helped me and Dr. B learn a lot! Lots of love! 

Bonnie, what are your other options if you quit? Anything promising?

Do what you need to do. Trust yourself. Dr. B is not going anywhere. You can return when you like.
I have just read a lot about joint pain in the forum. Seems like it's part of the healing process. I hope those that have complained of it, got better. It's hard to know since they are not around anymore. 

check this out-
http://www.icama.org/blog-entry/symptoms-related-changes-body-balance