Richard, have you been seen by a Rhumatologist?
My mother had trouble absorbing B12 and it had to do with her digestive track. She had to receive regular B12 shots. She had a different autoimmune disease that affected her G.I. tract. Her symptoms do not sound like yours however; B12 or any vitamin deficiency could have a GI issue to blame.
I'm sure they checked your anti-nuclear antibody (ANA)?? This test tells us we have inflammation going on somewhere such as Rheumatoid arthritis or autoimmune issues where the body may be attacking itself.
Please keep us posted.
It could be a lengthy process to find the culprit.