It is really difficult to give you a definite answer about your son without being able to see him. It is unusual for a child of this age to have complaints about pain and discomfort with no real cause.Young children are not usually hypochondriacs.It really would be a good starting point to confirm or discard the diagnosis of immotile cilia syndrome. You need to take your son to an experienced paediatric pulmonologist. If you are in the Gauteng area I can recommend Dr Andre Van Niekerk at the Clinton Clinic in Alberton or Prof Robin Green at the Steve Biko Academic hospital in Pretoria.
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