I would consult with a gastroenterologist. The can search for infections that may not be as obvious as most doctors would like. With stool samples and other more invasive tests they can look for a viral, bacterial or fungal disorder. The bowel and intestines can do really amazing harm undetected. They can affect the entire body.
Second...Consider an infectious disease specialist. They are the medical detectives.
Third...If you have not already had one, I would ask if a lumbar puncture (spinal tap) may be of help. Many infections and diseases can be detected through the cerebral spinal fluid (ie meningitis, encephalitis, west nile, lots of neurological disorders). I know of a few people who had viral meningitis and that manifests itself much differently and alot of times slower than bacterial). Thankfully it is also less dangerous.
I have learned that some doctors may give up on patients when they can't come to a resonable conclusion. Sometimes a diagnosis is more like a process of elimination. Some doctors will only look for the "common" problems.
You need to be your own advocate. Don't let the depression stop you from trying to feel better. There is a doctor out there who will help.
