It sounds like your dog has kennel cough. It's like the common cold in humans. The antibiotic treatment should clear this up for him. Keep him hydrated by using some plain pedialyte in his drinking water or if he won't drink it that way, you can give him some via dropper direct. You can also use a humidifier to help ease the symptoms. If you dont' have a humidifier available, you can run a hot shower and allow him in the bathroom at 15 min intervals to breathe the steam. Talk to your vet about using a pediatric cough syrup to help remedy the symptoms.
It normally takes about 2 weeks to run its course :) The cough can also cause some throat irratations causing the whine like noises you are hearing. Keep an eye on him, if he starts to cough up a mucousy discharge and is having alot of trouble breathing, call your vet as this may have turned into pneumonia...not very common but it can happen.
Good luck and hope your boy feels better very quickly. I also wanted to say KUDOS TO YOU for getting him to the vet and tested for all the other possibilities that could have caused this :)
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