Shell, that is cool stuff. Those are the steps forward, the pain is the step back. Although I don't have MS I have had this too... Pain in my joints that had not given me any trouble before, pain in my lungs which was a big surprise, a sudden attack of Carpal Tunnel Syndrome, an increase in numbness of feet and hands, more hair falling out etc. Ella on the other hand did not have pain, but her relapse took a nose dive and she had to be admitted to hospital as she could not breath.
It does take time to get some sort of understanding of what is happening to you. I think it took me six months before I could recognise a die off effect from generally feeling crap.
But in time you will know what is going on. In time you will feel a lot better about putting up with the pain and blahh feelings because you will be certain that it is making a difference.
I'm not a doctor or even remotely medically trained so what I say is purely from my reading, understanding and experience which is limited to myself and my daughter, plus the material found in the other place. BUT take care not to stop and start too often. I understand you have been in a lot of pain and anguish so it is right that you do what is best for yourself.
Just don't stop and start too often, it is better to reduce the dose than to stop taking it altogether.