I agree with luckies4me, could be a mite infestation. Maybe he could also be reacting to some substance or a type of bedding that irritates his skin.

Tia had some bumps similar to what you described on her left flank a while back. They were tiny bumps in three almost perfect lines. They didn't last very long, a couple of the larger ones scabbed over and soon fell off, the others just went down. I put it down to the fact that she could either have been scratching or cleaning (she sometimes cleans herself by licking her toes and then scratching) and just forgot how sharp her claws can get!