Help for excessive gas

Hi I'm asking for some insite on food for a 12 week old German Shepherd. This is my son's puppy. He was recently treated for Parvo and is now home. He's had feeding issues since birth though and they continue. He becomes extremely gassy after eating and his stomach gets bloated. The vet has him eating Purina EN and he has a medication to move his digestion quicker Reglan. He is also taking Flagyl and Acidophilus. None of these solutions has given him any relief. The poor puppy moans in pain after each meal. All his lab tests are negative.
I'm hoping someone has some ideas that might help this poor little guy.