Hmmm....my Stewie adjusted pretty quickly, but I think it's because the breeder had several children and the puppies were in the house with them. Are you working on commands? Right now with my boy we're working on "come" - this seems to be the one we have the hardest time with.
Is he a tiny baby? My Stewie is itty, and also seems to cower when we reach out to lift him. What else is your boy doing that makes you think he's taking a while to adjust?