Poor baby. Thank you for taking him in....in time, he will come around. He has been through so much.
I would provide him with a safe place all his own....a bed in a quiet spot...or even a crate with soft bedding where he can go off to be alone. As suggested, taking him out for walks and play time is good ... but I personally would not push that too much for right now. He really needs time to mourn...and to realize that his life, while different, is safe and loving. He also needs to recover from the kennel cough.
Even if he was debarked, he could still make noise. I am sure this is temporary...he will probably be yapping away within the next couple of weeks. I have had many pups come to my home and be so quiet and then end up the loudest of the bunch.
Welcome to YT! Looking forward to hearing more about your new baby!