You can have acid reflux even if it does not show in the endoscopy. An endoscopy has to be done on an empty stomach which is less likely to be "active" and producing acid because there is nothing there to produce acid over.
Have you ever tried taking an over the counter antiacid when your stomach hurts? If taking something like Gaviscon makes the discomfort go away, it is then possible that you have some type of reflux or acid irritating your esophagus. The Gaviscon would temporarily coat the esophagus and ease the irritation.
I have no medical training so you must take what I say with a grain of salt. But when I had my endoscopy, my GI doctor told me that she was looking for irritation, HPylori and cancerous/precancerous cells, but that the endoscopy would not be a definitive test for reflux. I believe they can perform other types of tests to see if you have reflux. You swallow a small probe and they can take acid readings through a 24 hour period.
I am sure there is an answer to your symptoms. Doctors have become so specialized that they stop looking and pass you on when your problem is not within their area of expertise. Doctors just don't practice integrative medicine anymore.
Hope you feel better soon.