If you don't trust the vets you are seeing, please get her to a university vet for a second opinion. Have you talked to any of the other owners of the litter, or is she a rescue?
When kennel cough is really bad, it can take months to clear up and the cough go away. She could also have allergies affecting her at night.. where does she sleep? Can you change where she sleeps to see if it's better?