The simple view of the bonding in methane You will be familiar with drawing methane using dots and crosses diagrams, but it is worth looking at its structure a bit more closely. There is a serious mis-match between this structure and the modern electronic structure of carbon, 1s 2 2s 2 2p x 1 2p y 1.
The second reason for a low vitamin D is that you have primary hyperparathyroidism due to a small tumor in your neck and the body converts all the vitamin D-25 (that your doctor is measuring) to the active Vitamin D-1-25 (that doctors do not measure). This is the blue blob on the graph.
But many people who avoid meat don't become deficient in vitamin B12. Many other foods, especially fish, contain vitamin B12. There are a couple of diseases that could cause low levels of vitamins D and B12. Celiac disease (gluten sensitivity) might cause vitamin and mineral deficiencies without specific symptoms. Crohn's disease could also cause both, but most people with Crohn's will have symptoms such as abdominal pain and frequent stools.