I just got back from the Vet; he said probably auto immune, but could be the plastic food bowl. I got rid of the plastic bowl and the pup has started antibiotics. If there's no improvement in 4 to 5 days he'll start prednisone. I did research after posting this question here, and it looks like "puppy strangles" which is a rare auto immune disorder in some pups, though it could also be an allergy to plastic.
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