If it were my son i would scroll to the top of the page here on the medhelp site and re post the same question under the "ask a doctor" forum. Those docs i understand hail from the Cleveland Clinic one of the best in the world and have long tenacles in the medical community....if one of the docs reading your question doesn't suspect something you can bet they will ask some of the other doctors....maybe that will help i hope.....they are pretty good about answering fairly quickly...Godspeed to you and your son and i hope you get the answers or at least an idea of the direction you should go in......
Has your son had an at home heart monitor? Did the doctors rule out anything with his autonomic system?
I've had some unexplained fainting myself that I am still trying to get to the bottom of. I will usually feel sick to my stomach then lightheaded. I get a long prodome so if I feel these symptoms coming I immediately try to sit down. If I do sit it will slowly go away. If I do faint, my eyes are always open and I do get a headache afterward too. Initially doctors told me it was due to bradycardia but that has since been ruled out for me. Anyway, don't give up trying to get to the bottom of the this. Good luck.
It sounds like you are getting the best medical advice, sorry that hasn't come up with a cure.
What is your son's "life style".. can you and he identify anything he is doing with the episodes you describe? I'm sure your doctors have gone over all this with you, but given they haven't been able to "measure" anything that would explain it, it may time to revisit all activities your son is engaged in, from diet to physical and emotional activities.
Hope you come up with an answer, and that others on this community will be able to offer more helpful inputs.