D.B.
If the ultrasound has ruled out constipation and blockages (and, I presume, appendicitis - even though I wouldn't think that pain would go away), and the echocardiogram was negative, you've ruled out a lot of things.
You have advocated well and seen several specialists. I can understand why you are annoyed that one GI specialist says he's fine if he's pooping and not vomiting. I can understand why you don't want to use a strong medication long term.
What I can't understand is why you won't try the medication. Sure, you don't know for sure if it's acid reflux. But it's persistent, and if you used the medication short term (as directed, no skipping doses, but maybe for a month or two, which is what they recommended) to see if your son gets relief, that would make so much sense. Of course you don't want to scope him - by why are you even leaning toward something moderately invasive that would require anesthesia rather than try a medication?
You can/should make dietary changes, and you should check for parasites as others have suggested, but the fact that this pain is exercise-induced but apparently not related to breathing difficulties would seem to me to rule out certain things.
I think you either have to try the meds for 6-8 weeks with some sensible dietary changes or you have to go to a children's hospital and put him through a much more extensive battery of tests with a multi-specialty team. But my guess is they won't look too kindly on you for not being willing to try something relatively simple - you have every right to question and demand answers, but if you're going to ignore a lot of advice, they're likely to give your child's spot to someone else. That's just the reality.
Your poor child is miserable - please use your options.