Can you get him tested to see what his allergies are? Then you could work on eliminating the source, rather than just treating the symptoms. It does sound like allergies to me, but that's probably because I am an "allergic person" myself.

I'm guessing your vet would have checked for FIV, etc., but did they?

Have you spoken to the breeder you got him from, to see if any other the other kittens have this?