hi...this poor kitty, can only imagine how irritating this is...you are right it is an allergy, to the food or litter usually. are you using scent free litter? eliminate all perfumes that kitty comes in contact with...even floor and carpet cleaners stick to vinegar...
if you are feeding dry food stop and switch to a 'grain free' canned...grains in food are often the culprits.
I will send you links to some older posts on the same subject, its a very common occurrence.
It could also be flea allergy dermatitis. Be sure he is on a vet-approved flea treatment like Revolution, it MUST be safe for kittens, and don't use the ones you can buy at feed stores and grocery stores, they are often not safe at all.
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