Whitney, You are giving your baby mixed messages by putting the pee pad in the crate. Put only soft, cuddly material things in the crate with her. You don't need a littler crate, just put a large object like a box or a large plastic container in the back of the crate and use the towels to cover it for comfort. Give her enough room to turn around and to sleep comfortably.
Continue to take her outside as often as you can, and stay with her with treats..we call them cookies, in hand. Walk with her in the area you want her to do her business, talking calmly, and praising all good behaviors.
Our male was very hard to train so during that time training time we got washable diapers for when he was in the house and he learned after awhile he didn't like the diapers so he went outside. You may want to try the diapers when she is inside for awhile.
The shaking and shivering is really sad. If she was abused physically or emotionally, training is going to be harder, and you will need to have a lot of patience with her.
The sofa she has peed and pooped on needs to be cleaned really good and that area of the house that she has marked must be off limits for her right now...maybe a fence at the doorway? Limit the rooms she is allowed in so you can keep a close eye on her while she is in the house.
Yorkies are smart, and she will learn, it might just take some time and patience on your part. Please give her a hug and kiss for us, and tell her we will celebrate with all of you when she potties outside. Good Luck to both of you!!
