My situation seems a bit different. I get left side of head above the ear headaches that are piercing type that when they come are intense yet will not last too long. They can either be a sign of over excitability in my brain ( caused by stress, noise or other triggers) or a sign a seizure could come.

One thing I read in your post that I personally identified with was:
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When I was a child many many years ago, I remember having the head ache upset stomach thing in Gym alot. Now I can admit I just was afraid to do gym do to fear of having a seizures. A normal fear, yet one most teachers would not understand, as they do not most likely have seizures.

Hope things can sorted out for your son and he feels better soon.