I am so sorry you are experiencing so many problems. It is no surprise with lingering pneumonia, nalabsorption and two autoimmune problems that you don't feel at all well.
First the B12. Have you tried sublingual methylB12? You can get this over the counter or online. This bypasses the need for the gut to absorb it - you let the tablets dissolve in your mouth. The pernicious anemia forum on Healthunlocked would have a lot of people who have tried this. I understand that research evidence shows that taking B12 by mouth is as effective as injections, and I think it is unlikely to do any harm to try this, since the B vitamins are easily got rid of by the body. And your symptoms sound as though B12 may well one of the problems. You then can dose to see if your symptoms improve without having to plead with a doctor.
Iron levels - this poor absorption is due to your AIG, but I expect the fact that you have pneumonia may be playing in. When you are chronically ill the body also restricts the absorption of iron, because bacteria and viruses feed off iron. I read in research studies that "anemia of chronic disease" is very common in hypothyroidism.
The thyroid needs iron to work properly, so you are trapped in a massive vicious cycle.
If they can deal with the pneumonia, then your body's resistance to iron should reduce. However, you still will have autoimmune gastritis. I think you will need to take iron supplements in the most absorbable form then - and you will need to ask them to keep a very close eye on your blood count and your serum ferritin.
But the B12 I think you should be able to help now.