It's a fair while since you posted this request and the issue has hopefully been resolved by now.
On one of the other pyloric stenosis discussion pages of this site someone posted their story (10 March 2010) of discomfort and pain leading to gall bladder surgery only to find the GB was fine but that the PS surgery he'd had in infancy had left him with severe adhesions.
Around various websites there are many stories of ps surgery (esp when done under the right ribcage) can result in discomfort, tightness and pain in later life. Any significant surgery in the abdominal region can result in adhesions. Whether to leave them or re-open and quite likely cause more of the same problems in the question.
I can't suggest any docs, but has he been evaluated for gallbladder issues? Spasms of the common bile duct or the opening to the duodenum (sphincter of Oddi) can cause a backup of bile and pancreatic juices and that can result in pancreatitis. Has he been rechecked for on-going problems with pancreatitis and have the monitored his liver enzymes and pancreatic enzymes?
When they did the scopes, what did the reports say about what the biopsies of the duodenum showed? Inflammatory patterns can result from more sources than just acidity from the stomach. Is there any history of celiac in your family?
If you haven't read the biopsy reports yourself, get them and do so. There could be some 'clues' hidden in there. Docs often pass off an inflammed duodenum as being due to acid alone. You need to make sure there isn't another reason, which means reading those reports.