Hi there. My Yorkie always cowers when we bend down to pet her or to pick her up. I think some of them are just like that because of their size. Try always kneeling down to her level on the floor before reaching for her. That seems to work with Mandie..she won't cower that way. She does run away sometimes. I think they all just have their own personalities and Mandie is the kind that loves attention when she asks for it but other times, she wants to be left to her own wiles. lol
To get her to play and interact more, try enticing her with little treats everytime you play with her and the toys. She'll start associating playing with you and her toys as extra special because she also gets treats. Work with her to teach her tricks with treats, too. This will give her a sense of accomplishment and might bring her out of her shell some.
And, as you said, she might still just need more time to adjust too. Be patient and just love her as you do. She'll be fine
There are members here who have worked with rescues and I'm sure they will offer some good tips and advice for you.