Stomach issues and gluten
I know you mentioned that your daughter forgot her meds for lunch and caused problems but once that time should of passed and still had issues. One thing that all should consider that have consistent GI problems even when you do take your pills is that you might have gluten sensitivity or actually celiac. CF issues mask many other problems. 30-40% of the population have gluten sensitivity. I had chronic GI problems and the only solution the docs could offer take more enzymes, take antacids, take PPI's, etc etc. Not until I went gluten free that my bowels went 180 and I actually had good poops. So her pain and fever could be other issues going on. Google "Dark side of Wheat" and see what is written about CF and wheat.
I noticed some others stating about how she is shorter than her sibling, this is also suspect and would behoove to look into.
I could not tolerate fats before also, there was too much inflammation and damage that the fats would just slip through. Now no problem I can load up on high calorie fats and obvioulsly have to take my enzymes but no comparison as to before.
Also daily probiotics is essential for all Cf's and Vitamin D, L-glutamine is good amino for the intestines and taurine.
To deal with current issues make sure she is getting lots of fluids that will help with moving things along and hydrates her. Also pepto bismol and such can help soothe irritated GI.