I understand not wanting pets in your bed. I am the same way - I don't think there's anything wrong with it, but I like my bedroom as my "kitten free" zone since they love knocking everything off of my dressers and attacking my feet under the covers. I'd be scared to squish them in bed too.
Where did you get the kitten from? The rescue agency I got mine from has been very helpful with any little kitten problems.
I think the best idea is going to the vet for your kitty's first check up. Take care of the fleas and also please watch for diarreah. If a kitten is stressed its easy to get coccidia. Its also very contagious so depending on the living conditions and general health of the kitten and its littermates in his first 6 weeks, he could get it. Ask you vet about the crying too.
I wouldn't punish him by spraying him with water. Is there any way you could section off an area for him in your room with a large dog crate or x-pen?