KMBR, you might just have pouchitis, which is usually easy to treat. You will need to find a doctor, though, preferably a knowledgeable gastroenterologist. Another possibility is a C. Diff infection, for which you'd also need a doctor. Ordinary gastroenteritis would generally have cleared up after two weeks.
You could try a good probiotic, like VSL #3, in the meantime. It might help a bit. Good luck!