Technically cats don't have retractable claws, they have extendable claws. Meaning, the natural state of their claws is the withdrawn or "retracted" position. They have to extend them in order for them to be out, normally, so I would say there may be some sort of issue in the feet of a cat that always has their claws out if they are totally extended and not just sticking out a bit past the sheath.
As for your kitten hurting you, all the activities you mention are ones in which a cat would normally extend his claws. My guess is that your Kabou has learned that it hurts you when she uses her claws, and Brandon has not. You pretty much just need to teach him that he is committing a social faux pas when he uses his claws on you, that it hurts you pretty bad, and that us naked apes bleed and hurt when they use us a a scratching post.
The best way to do this is to completely overreact when he uses his claws. If Brandon is a shy or not totally adjusted cat, this probably isn't the best idea, but if you have a good relationship and he is a normal, confident, loving former shelter kitty, then it should work really well. Everytime Zissou used her claws on me, I would yell "OW!" (not like you are mad, like you are seriously hurt, think papercut in the eye) and then hold where she had scratched and pretend to cry. Never punish the offending cat, though. Zissou will absolutely not use her claws on me ever, not even if she's falling off my lap. She knows it hurts!