Need help with orphaned puppy?!?!?

I want to start by saying he is three days old, and is the runt, The mother rejected him yesterday. We attempted to help him back but we can tell she feels discouraged with her milk as that he was a littler a five and she only has four good and gets very stressed by his crying. She started to become violent and bite him so I just took him out the of the litter and now she is doing great. My vet gave me all the tools about feedings and nutrition and he is doing wondering but his sleeping is terrible. I got his bed very comfortable, heat, fuzzy nest blankets so he feels snuggled but he only sleeps in my hands or if he is touching my skin. I wouldnt mind at all, but I can not always be holding him. How can I get him used to his box or is there a substitute to me that might make him feel at home. Since he does sleep on my chest I put a small clock in his box that ticks, to simulate a heartbeat but its not working. He still cries so much, I just dont want to stress him..