You make some very good points about doctors communicating with each other. If you have a large inter-disciplinary medical center near you, like a university medical school or a Mayo facility, you will have greater communication between your different physicians as long as they are all part of the same center. Since you go to the VA, you might be able to get records from each doctor after your appointment and bring them with you to the other appointments. It might seem awkward at first, but it will be better for you in the long run.
As you are having problems with a low Vit D and a high Vit B12, have you consulted with an endocrinologist? If not, this might be a good idea.
I'm looking forward to hearing from you again. Will you post an update?