I have experience with newfs, but I have got some words of encouragement. The breeder of my male Shiba Inu, Tonka, had a pup that required surgery to survive, she was only 4 weeks I think when she had her operation. Well because of the recovery time, and age she went under she was about half the size of a normal Shiba, about 10lbs, full grown, BUT she was healthy, she was just small. It sounds like the same thing happened to your guy, her mom had rejected her as well (the flung out of the whelping box part sounds like rejection IMO), but once she was healed she was fine.