Hi B.,
My daughter had the same horrible crying - up to four hours at a time. But it wasn't acid reflux or pain - she needed more intense soothing help than most babies. The only things that would soothe her was white noise and rocking and or car rides. The white noise was LOUD vacuum, LOUD ocean wave CD (cheap at Target) or running the hair dryer by her head. Swaddling also helped immensely.
Be very careful about treating her with medication - especially acid reflux medication. Yes, acid reflux exists in infants but it is rare. Make sure she's diagnosed by a doctor you trust (if it was me - I'd go to more than one for multiple opinions). I work in the health care industry and there is a lot of concern that acid reflux is too often overprescribed and that the medications for it are not as well-tested as they should be.
The book that helped me the most was "The Happiest Baby on the Block" that described the same type of unexplained colic that some babies had. This doctor's soothing techniques really helped me a lot. My mom is a RN who manages a program that gives nutrional and pre/post natal care to low income women - she recommends this book a lot to women who have babies who cry more than most.
Breastmilk is far easier to digest than any formula, so if you still have it, I'd give her that!! It may have seemed like your breastmilk upset her, but really it may have far more to do with the fact that her soothing mechanisms aren't the same as other babies.
But have hope!!! My daughter grew out of it, gradually crying less and less and now she's a very happy, intelligent little girl at four years old. But at 3 months, I thought she'd be miserable her whole life. In fact, she was a dream as a toddler - I never had screaming tantrums from her!