Sorry that your daughter is in so much pain. I agree it's probably good that calprotectin has dropped, but 1040 is still really high, and 3 Remicade infusions probably isn't enough to have calmed her inflammation yet. Is she on any other faster acting treatments, such as steroids or EEN? She may need a bridge therapy such as these until Remicade can take over.
My daughter was in and out of the hospital a few times during her first 6 months of treatment, and one of the times was for an abdominal infection that did cause her to have a lot of pain. The doctors thought it might be appendicitis at first, but they ended up deciding that her intestines were leaking into her abdomen via microperferations, which caused an infection that needed to be treated with IV antibiotics.
If your daughter continues to be in a lot of pain, I would consider taking her in to either urgent care or the emergency room. Sometimes when your kid has been sick for a while, you lose track of how bad things are getting, you know? In my daughter's case with the infection, we took her in to urgent care and they sent her straight to the children's hospital from there.
Hope your daughter starts feeling better soon.