First i'd look for a decent dr - one who'll check your daughter out thoroughly until the problem is found & solved.

Second though you could go to a search engine & look up each of her symptoms till you find medical conditions that seem to fit.

Third, you might want to restrict her diet further for a couple of weeks then gradually re-introduce foods one at a time several days apart & see if there's any changes.

Fourth, some of the symptoms like waking up stomache pains/diarrhoea etc could be related to stress over all this.

Last & i'm sorry for raising this spectre but is there any chance at all that someone (male/female, family, friend, teacher anyone) might be sexually assaulting her? The rash could have been caused by it starting as touching or "coming" between her legs & then as the abuse worsened so did the symptoms. I really hate suggesting this possibility but I have worked in this field so do have some knowledge of possible symptoms. But before you go out & kill anyone, these symptoms could also be caused by other things, including stress etc. Maybe take her to see a child counsellor/psychologist/psychiatrist??

My prayers are with you both.