We are going through this right now with our 3 year old daughter. She also has a fever that spikes to 102 at the same time.
At our insistance, our Pediatrician ran a series of tests and found D-Diff bacteria in her intestines (usually a result of having multiple rounds of antibiotics) and now we are on a 14 day round of a medicine to get rid of this bacteria. It was a simple stool sample that we collected at home that got us this diagnosis.
It really helped us to document when she was getting sick (what she was eating, any other symptoms, any changes in her environment, mood etc) around the time she would get sick. It helped to see if there was a clear pattern or cause of her illness.
I would also say that you should push form more testing. We also looked at Celiac Disease, and other GI disorders. We saw a pediatric GI specialist as well.
Our daughter may not have the same symptoms as your son and has been sick on and off since August and lost about 6lbs which is a lot for a 32 lb little girl, so please don't be alarmed by our story, (everything is very treatable and usually non intrusive) but if you are feeling like the answer your doctor is giving you is not the right one, go to another doctor or demand a closer look or second opinion.
Doctors aren't always right.
Good luck and I hope he feels better very soon.