I was diagnosed with adult onset anaphylaxis about a year ago when i graduated high school. My case is severe, with over 20 allergies including 4 of the top 8 so I've got some experience. Allergies suck. Let me just tell you that... but it does get better. When I was first diagnosed, I was afraid to eat anything. I literally lived off of organic dried blueberries and water, NOT a good idea. I started to feel really crappy; fatigued, losing weight, tired and my appetite decreased. But as soon as I did more research and found other options I could eat, I gained weight back and started feeling like me again. As far as changing your diet, any drastic change, even if its not as drastic as mine, you're going to notice. You might feel off for a while, but it DOES get better. Once your body adjusts to the changes you'll stop having stomach and fatigue issues. I can't put an exact date of when you're going to feel better, just reassure you that it will happen. And one more thing, I have a wheat allergy as well and you need to make sure you look up all of the names for wheat, online. Sometimes nutrition labels hide wheat ingredients or ingredients that contain wheat and they're overlooked. Be careful, make sure you read your labels, and feel better! AND, you're in luck. Gluten-free is the new black. :)
You may well be missing something; also, your body is readjusting. Use the internet to make sure anything you are taking does not contain your allergens. Also, tell your physician about your fatigue and stomach issues. Good luck and keep me posted.