Welcome to pet talk!

If he is not eating & has all those symptoms I would make a re-check appointment with your vet, or at least call & explain to them what is going on.

It does seem as though your vet is prescribing the right meds that are mainly given to dogs w/ those symptoms, for some reason it is not helping your pups. I suspect something else may going on. The pneumonia will take a while to get rid of though. But the kennel cough takes a while to get rid of you should not be seeing him that lethargic, not eating etc... after 3 days on the meds. He should be perking back up.
Since you have battling this problem, mainly with Nala, but now with both dogs for a month & still no improvement I would probably seek a second opinion, especially for Nala.
Did they do any blood tests on her?
Kennel cough will usually go away left untreated if it does not turn into something worse, like you said w/ Nala, pneumonia. BUT with smaller dogs, they seem to get sicker faster & easier *usually* unfortunatly.

The food change may help w/ Nala's stools.

I hope your babies get better soon!