It's a fair time since you posted and updated this. How has your son gone since?
From what you mention I thought of 2 possible causes that others on the MedHelp pages have posted about after effects of PS surgery.
One is a problem with the scar (hernia, rupture or stitch residue). One man I've corresponded with still had bits of thread emerging from his scar after 45 years!!
The other is adhesions, which 90%+ of us have after abdominal surgery. If severe enough these can cause the kind of problems you list, and worse. One poster on MedHelp had to have the adhesions after her pyloromyotomy cleaned up at age 5, again many years later, and she fears she may be heading for the OT again.
See your doctor if these problems persist and push for an answer.
These are good reasons for doctors to consider the medical alternative to pyloromyotomy more seriously when a PS diagnosis is non urgent.
Oh well, he hasn't had any symptoms since I posted that so maybe I was worrying for nothing.