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It's not a matter of getting his stomach working properly, it's in some measure a problem with getting everything to move down, and not have anything move it back up into the stomach. Part of it may be that he needs to remain upright - standing - for some period of time after eating. Even sitting would place pressure on the abdominal cavity and that could encourage movement of foods back toward the stomach.
You may what to ask his doctors to refer you to a nutritionist to give you a hand with this. It may be difficult to find a balance in the foods he can handle due to the whipple in addition to making sure he stays away from gluten-containing foods.