First of all, I am sorry to hear you are suffering so much! You can take comfort in knowing that you are probably not alone in suffering from this disease, even among runners in the running world. There are a lot of well trained athletes who suffer from a myriad of illnesses that would otherwise hinder them from what they love to do (i.e. run and be active) if it were not for a proper diet, good doctors, and a fantastic support system.
I think the first place to start is knowing what your disease or illness is. With that information, we can provide for you a more tailored approach to what you should eat to fuel your running while still allowing for what you CAN eat. Also, I would advise to listen to your doctors. I totally understand not wanting to take a pill to cover up your deficiencies but sometimes taking a supplement to help make up for what you are not getting through food and nutrition is the easiest, and most economical and practical way to ensure you stay healthy, avoid injury, and can run. While it might not be completely ideal, my advice would first be to listen to your doctor and do as he or she tells you.
Secondly, your list of foods to avoid might seem long but fortunately you can certainly work around those! You have probably heard that the body primarily runs off glucose to fuel its functioning. This, in short, means you need to focus on carbohydrate sources in order to have enough glucose to fuel your running. While it looks like you can't have most fruit sources of carbs or wheat sources, carbohydrate sources that come from other starches like corn would be an easy solution for you. You can also get creative with your snacks and meals, going beyond just boring old corn on the cob. Try incorporating popcorn (served straight up or as part of a trail mix), corn tortillas, or other corn based products into your meals.You also definitely need to incorporate meat into your diet, not only to increase your iron and other intake of vitamins, but to pump up your protein. Protein will you recover better, and grow stronger.