Might be worthwhile looking into your MTHFR genetic status as it can be involved with Vitamin B12 deficiency (and other issues) - are they also doing testing for folate and intrinsic factor status?
I think you may find you're being unduly pessimistic about possible improvements - when you get your Vitamin D3 status back to normal, I think you'll be surprised by what a difference it can make to your general wellbeing. It made a huge difference to me, though I didn't have the extra complication of B12 to deal with as well.