--that the lab results do suggest an ongoing B12 deficiency (and there may be other low B vitamin levels as well), I do think that the autoimmune possibility should be checked out further.

Certainly, B12 deficiency and autoimmune problems often go hand-in-hand ("pernicious anemia" caused by lack of intrinsic factor, leading to lesser B12 absorption, typically results from autoimmune processes), and the chances of having more than one autoimmune process going on are fairly high. You should have the ANA result further checked with more specific tests for type and pattern (if you haven't already) and I would also get a celiac panel (anti-glidain IgG, anti-gliadin IgA, anti-tranglutaminase IgA, total IgA--deamidated forms if you can) and thyroid function panels (TSH, free T3, free T4, antibodies done (if you haven't already).