Thalminorguy,
I would suggest higher doses of vitamin D and L-methylfolate. My D level is quite high, as I want it, and it took taking 50,000 IU once weekly to get it where I want it. I am on a high dose of folate daily, 8000 mcg and it is the only thing that gets me through the day. I would not hesitate to take B-12 daily. I am also on a very high, 5000 mcg daily dose. With my thyroid, I have found that folate and B-12 are required for me to get through the day. Magnesium is also recommended. As far as kidney stones, it might be advisable to avoid foods high in oxalates. Good hydration is also extremely important at all times. Turmeic capsules may help with the body pain. I take it morning and night to relieve chronic joint pain.
I want to mention that your RDW is borderline for iron deficiency and it may be helpful to make sure you have adequate iron in your diet. Even though supplements are usually contraindicated in thal minor, a diet that contains adequate iron is necessary.