Dogs (and puppies) rarely show pain. It’s instinct to try to mask it because they would be either killed or abandoned in the wild for illness, disease, distress. A good sign that he is in fact in pain is the loss of appetite. . He could have fractured something, causing the limp. Is he holding his paw up frequently? The pain could also be a sign of something else, like kennel cough or viral/respiratory issue. Has he been fully vaccinated? Perhaps a case of Pano? Just throwing options out there.
As for the food, if they are very small pieces of kibble, they sometimes inhale them instead of chewing like they do the rest. Seiran is on a large breed formula, but the pieces are tiny, and she does the accidental inhale every once in a while. She hacks it back out and continues eating.
Are you relying on touch for a fever? Dogs temps run higher than humans, and often feel feverish if you’re comparing it to a humans fever.
Good luck, let the vet know everything you’ve posted here, and let us know how it goes.