It sounds like you have more than one circumstance that your puppy is trying to deal with. The first few days after you brought her home the fluctuations in food and water consumption were due to the changes in environment and routine. Most puppies need 2-3 days to regroup. The second change in appetite and attitude are likely due to the respiratory infection that your vet has recognized and begun treatment. It usually takes about 72 hours for a response to therapy to begin, be sure to let someone know if she is not close to normal after a few days or especially if her attitude or appetite deteriorate more.