Help! New fearful dog only goes to the bathroom in her crate

Hey all! This is my first time posting in this forum but I really could use some training advice.

I'm a vet student, and a few days ago I adopted a dog from my school who was used for teaching purposes her whole life (she's now 5). She wasn't abused or anything, but she's lived a very sheltered life up until now so everything is scary and new to her. I was under the impression that she had some fear issues, but got along with other dogs and is still a happy playful dog.

Well, turns out she has the most severe fear issues I have ever seen - she's literally afraid of everything, every sound, if I move too fast, the rocking chair, my laptop, the outside, the inside, etc. You get the picture. And she's is especially afraid of my other dog who is very friendly and happy-go-lucky. He mostly just ignored her but she would run away from him every time she heard his collar jingle. She was so afraid of him that I ended up having to send my dog to my parents place for now, until she at least calms down in the house a bit. She's still scared of everything, but at least will now lie down and relax now that he's gone.

Anyways, the first big issue I'm trying to work on right now is that she is so afraid of everything she won't go to the bathroom. I've had her since Saturday and she's urinated and defecated twice - both in the middle of the night, in her crate (which is an appropriate size for her and I can't really downsize it without it being too small). I think she is just so nervous and tense all the time that she can't relax enough to go to the bathroom, except when she's all alone in her crate at night. She's eating and drinking fine, and I'm taking her for walks and letting her outside constantly but she won't go outside. She wears a collar that is infused with calming pheromones and I've been giving her therapy treats that are supposed to have a calming effect on dogs. We've been doing "confidence building" exercises as well. Right now I'm on Christmas break so I'm home all time, but soon I'll be back in school full time and I can't continue to clean and scrub her crate and her every time she's left alone in it for a few hours. I have no idea where to start with this sort of training. Does anyone have any suggestions?