I found a thread that you maybe able to get some tips from. I have a rescue and these tips helped me tremendously as my little one was skittish along with a few other odd behaviors.
http://www.yorkietalk.com/forums/gen...nt-advice.html
Hope it helps and congrats on your new puppy. It takes time but love and persistence is the key. When he feels safe and secure, you will begin to see him blossom. I should know I now, my little one went from being afraid of her shadow to a bona ride diva.