Since I'm not a medical person and I've self treated, it's interesting to here someone's opinion who has such detailed knowledge of the systems involved even though I have a different conclusion on the cause and therefore treatment. It seems there is always more to learn about this. I haven't looked into inflammation or food allergies much in the past.
Here is how I've incorporated inflammation into my understanding and finally addressed what is causing the chronic fatigue. I've talked about how the mind signals for the "freeze" response under stress and trauma. There are several subconscious reactions including clenched muscles, an adrenaline surge, etc. We know this from our experiences. When something is coming at us we brace for impact or when we feel embarrassed or shameful we might notice that we are clenching if we bring our attention into our body in the moment. These reactions are imprinted on the mind in the form of unprocessed stress and trauma. I'm sure many here have felt tightness in their muscles in some form whether it's TMJ, back or neck tightness, or in parts of their legs (restless leg syndrome). This is the main source of inflammation (fatigue) in my opinion. When we work out and inflame our muscles, we get fatigued. So it makes sense that we would suffer at times exhausting fatigue if our muscles have been clenching (if not at present in your body now, then below the surface) for as long as we have been ill. This is why I'm curious how your doctor concluded the brain is the main source of the inflammation.
I just did some reading on food allergies and I suspect there is a connection with it as well. It seems food allergies are when the immune system rejects a specific protein found in certain foods. It's basically an overreaction to something that isn't harmful. People are told that they need to avoid these certain foods now.
What if the problem is not with that particular food but with the immune system itself? We know that the immune system is connected and affected in all of this. I found that people can develop food allergies later in life that they didn't have as a child or they can even have a food allergy , lose it, then regain it again. This is telling me that food allergies are a symptom of this illness and not a cause. Is there something I'm overlooking here? I don't think it's a coincidence that food allergies are increasing in recent time just as mental illness is (I use the term mental illness very loosely and inclusively).