Having read your question, I am not going suggest what you say isn't working. You are right, it is the stress of begin left shut up alone. I have had good luck with leaving 7 week olds 4-5 hours in a crate with few accidents. Since Saturday, our Xanthe is 5 for 5 for making it over night. Surely the shelter didn't let you have a puppy much younger than that.
Unfortunately much of what works in some cases, isn't working for you. Since I have never had the problem, I can't give you what worked for me. Nor is it in my Puppy Raising Manual. In the sticky at
http://www.askmehelpdesk.com/dogs/in...tml#post251802 I talk about laying down in from of the crate and using a grid in it. They may help some. I am sure the problem comes from poor care before you got her. My manual does give ways of bonding and showing leadership which should help reduce the stress.
''Elevation for small puppies: Sit on the floor and gently put your hands around your pup's middle, below his front legs, and lift him up. He is facing you. Hold him for 15 seconds. Repeat until he no longer struggles. If he is past 10-12 weeks, lift his front feet off the ground, but don't pick him up.
Cradling for small puppies: Hold your puppy gently on his back, as you would cradle a small baby. If he struggles, hold him firmly until he quiets for 10-15 seconds. With larger pups, you can do this as your sit on the floor, with your pup between your legs.
Quiet lying down: Place your pup on the floor on his side, with all 4 legs pointing away from you. Use your hands on his neck/shoulder area and middle, to hold him in this position. When he is quiet, praise him. Lengthen the time that you keep him quietly in this position. When he accepts this position well, handle his paws and muzzle, while keeping him quiet.''
The quotes mean this isn't my original work. It is copied from my Puppy Raising Manual. I have long used these or minor variations of them, and they are very effective. You may want to give him a belly rub while he is on his back too. Helps bonding. There is a big difference between him rolling over and demanding a belly rub, and you choosing a time to roll him over and rub his belly. The latter cements your place as pack leader.
You could also talk to the vet about medication. It could buy time for her to develop trust in you and enjoying a clean crate.