Snakes will often make a whistling sound if they have loose skin in their nostrils that may not have come off during a shed.

A couple questions, though... Did you take him to a reptile vet? Did the vet give him a series of shots or just one shot? Typically, respiratory infections are treated with a series of antibiotic shots. I've never heard of just one being given.

You may want to just watch him to make sure it doesn't get worse or that he doesn't experience other URI symptoms, but I would still suggest that you take him back for a followup visit to rule out a chronic URI.