I think you are suffering from inflammation of various systems. Muscles and digestive system included, but probably others too. I've heard of some people finding relief by avoiding all foods in the nightshade family.
I still think you have one of the MTHFR gene variations that causes issues with processing amino acids and can lead to toxic build up of some of them. My research into this is still very new. Unfortunately, the discovery of that gene's involvement is so new that the medical industry has never heard of it.