First, welcome to Pet Talk! I'm sorry to hear about your little pup.
Could you try a different vet for a second opinion? I agree with luv4dogs, there could be something else going on. Has your pup been checked for parvo?
Even though giardia and coccidia has been ruled out for the loose stools, it may be worth it to run another sample with another vet. Also, perhaps a different medication would be helpful. Metronidiazole can be given for diarrhea, and is typically given for kennel cough, giardia...etc and other diarrhea causing conditions. It sure does sound like kennel cough to me.

Please let us know how they are doing!
**hugs**