Definitely do what your vet suggests!
The reason he is quiet is probably due to the Torbugesic. This medication is used for pain and also for coughing. Here is a link with information:
Butorphanol Tartrate (Torbugesic®, Torbutrol®)
If you think he is too sedated, you might want to speak with your vet about perhaps cutting back on the Torb. It is a great med for coughing ... I would think that after a couple of days on the antibiotic his coughing might decrease and you might not need to continue with the Torb.
I hope your puppy is better soon! Welcome to YT
You will learn a lot here that will help you.