My DS2 doesn't have what you have described, he does have a problem with his oesophagus though (Eosinophilic esophagitis). It was diagnosed with him having a endoscopy. A barium swallow was not going to find what he had and he had to have the endoscopy as he needed to look with a camera and take biopsies.

The worst part of the endoscopy was the going under and coming out of the an anaesthetic, he had to be fully sedated due to the endoscopy. The procedure itself didn't take long and he was only under for 30mins or so. He was particularly grumpy and disorientated for a while after coming out of it. Once that wore off he was fine.
He was 3 at the time of diagnosis so his understanding of what was going on was not great.

Hope your little man gets some answers.