That sounds like Kennel Cough, you should see a Vet. period ASAP!
We are all attached to our Babies, but in reality as a Consumer, if you paid that price for that puppy he should be in perfect health and have an incredible Bloodline, be AKC. registered, micro-chipped and everything! You need to stop being emotional and think with your head first & foremost. You might as well cut your losses and deal with all of your pets/baby's problems? If it's only Kennel Cough and finicky diet that's easy to take care of. But if something is seriously wrong? I would make the Pet Store pay/return/refund or something?
They are responsible! It pays to do research first. Sorry you had such a bad experience, Good Luck!