I too would check that probiotic - a lot of them have dairy in them. What about nuts? What "milk" are you drinking? some almond milk can have soy in it, and if it's a nut issue, the almond/coconut milk could also be the problem.
Have you had her stool tested for blood? Is there any concern that the crying/fussiness could be reflux from the food intolerances?
Katie's mucousy stools never cleared up completely when I went dairy/soy free. Oddly enough, they seem to have improved once starting solids (I actually suspect she's beginning to outgrow whatever other intolerances she had). But she didn't have blood in her stool anymore, and she was (still is) on meds for reflux and that addressed the pain that was causing the screaming. Our pediatrician said I could continue trying to eliminate things from my diet, or I could keep going as I was (dairy/soy free only) because Katie wasn't suffering long term damage (no blood) and her pain was managed. The GI specialist told us to quit bfing and go to amino acid based formula as Katie was allergic even to the protein in my breast milk. In the end, we decided not to stop bfing (for many of the reasons Shiv mentioned above) and she continues to get better. At 3 mos, I felt like we really began to turn the corner. We've not changed her meds in 2.5 - 3 mos, I've started eating goat cheese, and she's started solids and we've not had a reflux flare in almost 3 mos and no mucous in 3 weeks.