There are two pieces of good news here. The first is that you now seem to have a diagnosis, so treatment choices can be directed properly. It’s also probably a better diagnosis to have than chronic pouchitis. The second is that in the last few years an effective way has been developed to treat C. diff that doesn’t respond to Vancomycin. Fecal transplants are very successful In getting rid of stubborn C. diff infections.
Your test before surgery may have been a false negative, FWIW. Good luck!