Was Gastro-esophageal reflux ruled out?
It can cause chronic cough
, recurrent vomiting
, failure to thrive
If its there, medications are available which can help him.
Usually stomach swells up if there is an obstruction in the junction between stomach and duodenum
. From what you say, it looks like extensive investigations are done and surely major problems would have been ruled out.
If his weight and height are okay for his age and he is thriving well, his activity is okay, there will be nothing much to worry.
Hope my answer helps you.
Wish your son good health.