My son, when he was 2 months developed a cough and was very irritable. Two doctors couldn't tell what was wrong, but the 3rd diagnosed him with GERD (reflux). They put him on all kinds of medication but nothing helped. Finally, I called the La Leche League and they gave me alot of good advice for breastfeeding moms.
First of all, KEEP BREASTFEEDING!! My doc wanted to give him a special formula to make the food stick in his stomach, but that's the worst thing you can do. No cereal or anything, you want to empty his stomach as quickly as possible, plus breastmilk is the best thing for him.
Second, I took all dairy out of my diet along with caffeine (coffee) and chocolate. Within a couple days (and I took him off all medication) he was perfectly normal and happy. The doc even noticed a difference at the check-up when my son was smiling instead of screaming!
Third, make sure the prop up your daughter after she eats, have her eat smaller more frequent meals as that's easier to digest than a big meal, and at nighttime put towels underneath her mattress when she sleeps (if she gets irritable in the middle of the night). Also, I'd suggest getting in touch with a La Leche League leader as they offer a lot of good, practical advice that the doctor never told me.
Good Luck and I hope things improve!!