I adopted a 5 month old kitten from an animal shelter a week ago and the kitten has come down with an URI?

We took him to a vet and he was given an antibiotic, lysine, nose drops and eye cream. Lately, he has started to get really congested and is having trouble breathing. He breaths through his mouth and sometime he coughs as though he is coughing up a hairball. His eyes are more watery than they originally were and he is starting to become less active. At the vet, we were told that the infection just needs to run its course, but I am worried about his breathing. Are there any at home remedies to help him? I have tried running the shower and closing the doors with him in the room, but that only helped briefly.