I am with CT on this. You have plenty of info to point toward chronic pouchitis. The chronic inflammation likely led to the deficiencies. Prometheus results are a red herring and essentially meaningless. Diet may well keep you on track, but don’t rule out treatment in the future, or beat yourself up if diet does not work long term.
My B12 was also low and I responded very well to supllements. I only take it twice a week now and my numbers are quite high. My folate was always within range, though. My B1 and Vitamin D were also low. I always have eaten wide variety of foods.