You said, "but found it very uncomfortable so it was stopped." That sounds to me like your son was awake during the procedure? If so, get a new doctor because they knock you out cold when this procedure has been done. I've had it done twice in a hospital, and twice at doctors who specialize in the procedure, and all 4 times I was knocked out cold. I would not worry about a cat scan just yet. They just want to rule out possibilities. I have a rare lung disease called MAI and on xrays it looks just like TB and cancer, so they rule those out by having phlegm analyzed. Be patient and optimistic so that your son is also. Hope all goes well for him!
CT sounds reasonable. Alternatively, consider fluoroscopic esophagram.