Some things don't show up on CT scan, he most likely needs to have a scope where they can look inside at the lining of his esophogus, and stomach. EGD shows the upper part of GI tract, Colonoscopy shows lower part. He could have an ulcer or something like pancreatitis or gall bladder problems. He should have lab work that includes enzymes in case of liver or pancreatic problems. He could have a parasite too. Get him to a Gastroenterologist or take him to a children's hospital ER. This is not normal and getting hydration though obviously necessary to replace fluids, it isn't going after the problem.
Pancreatitis can be difficult to diagnose and treated by IV's, sometimes antibiotics, TPN and not eating. Those people often have so much upper abdominal/stomach pain. They can develop pseudocysts, but those should be seen on CT scan.
Let us know how it turns out, my heart goes out to him and to you!
RN