These are all good signs, especially the pooping and peeing in the box. It means his body can go on its own without being stimulated by mom or you.
As far as the eating thing goes, he may just not be ready yet. I know you are probably feeling a little panicked by this too. He also needs the warm touch and interaction that bottle feeding brings, which is probably why he is crying so much. They are a lot like human babies and "cry" to be cuddled and held. When you pick him up you probably notice he quiets down a bit, liking the contact and also knowing he'll get fed. Aww, poor little guy, I wish I was there to help you out greenthumbnails!
But to answer your question, he'll ween himself when he's ready to eat on his own. Some kittens still like to be nursed even when they are eating good on their own too.