Wow, you definitely have a mystery diagnosis in the works! At least you have a doctor who is willing to keep working on finding and answer and in the meantime give you some relief. I'm so glad the MS was negative!
Have you ever been tested for lyme disease? I had a friend who had a MS diagnosis for years, but when they did the spinal tap it was actually lyme causing the symptoms.
One other thing I don't think I have mentioned in a while is Pompe Disease. My doctor had been to a seminar last year where they talked about it possibly being confused with myotonia congenita because of the myotonic discharges on an EMG, but the DNA tests would come back negative. It's also covered by the MDA. It's caused by an enzyme deficiency and fortunately they do have a treatment for it. The symptoms can show up in infancy or as late as your 60s. It might be worth checking.