I agree with above suggestions but as well or ..................
I would talk to him a lot, just about whatever...let him watch you but acknowledge his presense by talking to him, like your talking to yourself, but your not! Especially when your feeding him and changing his water, litter, you already have his attention since your doing things that directly affect him.
Definitely allow him to come to you, but you can also coax him out by playing with him. There are a lot of fun interaction cat toys out that they love as well as help build a relationship between you and your kitty.
If he is that shy about petting him, the best is a long stroke from head to tail, this is the least personal area. Until more trust comes, then they love light head scratch/messages, chin, this is where thier scent glands are.... it really depends on the kitty. Maia loves pets all over, shes not the usual though!
As far as picking him up, this is something I feel very strongly about. Our pets should allow us to do so at anytime if there is an emergency so we can get them out of danger. BUT.....this is something that comes after a trusting relationship is established between both of you. So I would'nt push picking him up till hes ready. Most cats don't like being held, but they don't fight it if they love you and trust you as much as you do them.