I never produced enough either, even with pumping like crazy. Miles' had bloody stools @ 2-3 weeks, which meant milk protein allergy, so we switched him to soy, and I don't each much dairy anyway. Josh had respiratory issues (mucous build up in throat), which we thought might be due to reflux, then thought environmental, but we switched him to soy as well and it cleared up. He spit up/threw up the soy for the first week while he adjusted, so we tried different brands, and now he's fine with it.
The problems could be a manifestation of milk protein allergy. If you don't drink a lot of dairy or eat a lot of cheese, he won't get much milk protein from you, so it could be an intolerance of milk protein in the formula.
Keep having him elevated after feeding, and try to minmize movement/activity after feedings. Hope it helps!!!