Bless her heart. I wanted to pop in and say welcome to the forum and just continue the patience and love. If she does have some fear issues, the will eventually overcome them as long as you keep doing what you are doing and reassuring her.
A note, though, it is not uncommon for these Yorkies to cower when being called or trying to pick them up. My Mandie still does this. It helps to get down on the floor and call her instead of doing it all from a standing position. Even with that though...sometimes she still acts like that. I think it's just a trait they have.
With that said, though, shaking with fear is different so assume it is fear and procede as you are...with loving patience
