Here is a good thread for rehabbing a puppy mill rescue, and it has some good advice even if she was just heavily breed and not a pet per se:
http://www.yorkietalk.com/forums/gen...nt-advice.html
Time, and patience is your main course of action. Let her come to you, and do not force affection on her before she is ready.
Thanks for rescuing. Too many dogs do not get that second chance they deserve!!