I'm so sorry you've been feeling awful for so long. I am not sure exactly what it could be, but since you are working out so intensely and frequently it could be exasperating the problem. I hate to repeat what your doc told you but you really should take it easy.
I suggest going to a stomach specialist (gastroenterologist). I am sure that they would be more help to you than just your family doctor.
Just ask him anything that comes to mind. Make sure you ask him how you can help the pain in the meantime... all that.
Try to rest as much as you can. You seem like a really active person and I know that will really stink for you to have to rest a lot. But once this is figured out you can go back to your usual life- and better yet not be in pain!
I know what it's like to be sick and not know what is wrong. It's one of the worst feelings a person could have, in my opinion. If you ever need to talk or just vent I am here for you. Always.