I'd look into fructose malabsorption or SIBO (small intestinal bacterial overgrowth.) A hallmark seems to be low iron and high b12, and the bloating and fatigue fit with the typical symptoms.
I drink too much coffee. :/ There's a school of thought that says too much caffeine puts stress on adrenals, which may already be weakened by an autoimmune disease such as Celiac. This can cause a whole host of issues. If you do drink decaf, there are certain brands that are non-chemically decaffeinated, but I can't think of which ones right now.
I prefer caffeinated but I learned quickly to stay away from flavored coffees. Starbucks flavored something or other glutened me badly. I usually stick to whatever plain ol' French/bold/breakfast roast is on sale. Current favorite is Maxwell House French Roast. I also like HEB's store brand.