You may be gluten intolerant-yes I read that you eat gluten-free- however
you may want to also eliminate dairy, since half of gluten-sensitive people are also sensitive to dairy (look into Cyrex Labs for their details on cross reactive foods
I would also rule out low gastric acid levels-you may want to do a Betaine HCL challenge for that. Just follow the label instructions. If you consistently feel better, it almost confirms the low acid.
A negative result does not rule out the possibility of Helicobacter pylori infection, so pls consider doing another alternative test.
Finally, if the above suggestions do not point to anything specific, you may want to do a complete elimination diet.
Please keep us posted. Keep in mind that my comments are not intended to replace medical advice.