Valerie-
My son is allergic to both Milk and soy (and eggs, barley, legumes,
nuts...). He was never on any formula. He had daily explosive
diarrhea, which we learned (by RAST blood allergy test) to be from
Barley. What foods is your daughter eating? You may need to keep a
food diary, of times and symptoms. My son would crave the barley- eat
a lot of it, then the food would come thru within 3 hours. This
happened with dad's chili, too- the beans were in the diaper.
Gassiness can come from many substances, including fruits, and
additives in foods.

You didn't mention how old your daughter is now. Can she only eat by
g-tube? I have a friend whose child has allergies and has a feeding
tube. If you'd like, I can pass along email addresses.