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Eliminating gluten-containing grains from your diet can have dramatic health benefits, especially if your immune system reacts to this protein. However, if you stop eating gluten and don't feel great after a reasonable period of time, something is wrong.
One possibility is that you have not totally eliminated gluten from your diet. You need to be 100% diligent in avoiding gluten. Immune activation can last for months after consuming gluten one time. You could possibly be suffering from exposure to hidden sources of gluten. Do you lick the seal on envelopes? There's your source of gluten exposure. Do you use a toaster that has been used for gluten-containing food? There's your source of gluten exposure. Whether you are currently eating gluten or not, I believe the most definitive test for revealing immune activation related to gluten is Cyrex Labs Array 3: Wheat/Gluten Proteome Sensitivity and Autoimmunity.
Another possibility is that you are suffering a gluten-associated cross reaction to another food. A person can totally eliminate gluten from the diet but continue to suffer the health effects caused by gluten - as if the diet still contained gluten. A number of foods can cause the same immune response as gluten. What are these foods and how do you know if they are a problem for you?
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