WOW, that is a really young puppy!! I'm surprised they let it go so soon...Was the mother in the shelter also?
I have read that sometimes if the mother dogs are bred too early or too often, they tend to be aggressive towards the puppies, in effect teaching them this behavior is appropriate as they grow up. It happens often with puppy mill and pet store animals as they are often overbreed for a profit

It sound like your pup just needs a little more time to grow up and some good role models. I wouldn't even try training at this point but rather treat the pup age appropriately...and show it affection and love. Don't handle her too much, keep her in a comfy box, let her grow up a little bit more and still be a puppy before you attempt any serious training.
Also, you said she growled and bared her teeth when you handled her? Perhaps she is in pain...? I do not know if kennel cough causes pain but perhaps a fever? I know that when I don't feel well, I certainly don't want to be touched. But you said she was at the vet...hmmmm. I would just let her be a puppy for a few more weeks and try to show her love and affection at all times, no training, no reprimands...at least until she gets a little bit older.