Have you checked for H.Pylori or SIBO? I know your stool test has been negative but maybe try a blood test or ureea breath test. Many of your symptoms match a bacterial infection you already know my point. Its not alsways easy to find a bacterial overgrowth. It ttok me three years !!! Did you go back to Middle East?
Long standing infection goes to methylation issues. I for example have discovered I have CBS/SUOX defect caused by long standing H.Pylori and candida.
You might wana check what food causes these symptoms or when do they appear. Check for SUOX issues online and see if its matching yours. just an idea.