First, what a wonderful thing you have done to rescue a shelter dog. People are so into "Designer dogs" at the moment that shelter dogs go unloved, when they often have the most to share.
Second, German Shepherds are working dogs, intelligent dogs, dogs with a "mission" so to speak. And it is in understanding these things that you can help her.
When a dog has been abused, a lot of their natural instincts are quashed. Watch for what she is afraid of-- eg, the noises. Does she shrink from the phone when someone picks it up? Does she growl and bark at the newspaper, even when you're just turning the page? These are things my old shelter dog did, and it was incredibly sad to see.
Your biggest allies are patience, and love. Understand that, as you said, she really doesn't know what to do. So throw a ball for her, encourage her to run after it. And when she gets it, even if she doesn't do anything with it, praise her with a cheerful, wonderfully excited voice. You are going to have to be her biggest cheerleader in life for awhile. Show her how happy you are when she does ANYTHING that seems like play. As gross as this may sound (try it with a new one if she has already attacked one of her squeaky toys), put a squeaky toy in your mouth and imitate what dogs do with it, making noises and tossing your head around to show her it's okay to attack it. Push it back and forth between your hands, across the floor. Show her hot to play. Involve her a little bit, and if in the beginning she just wants to watch, let her. But encourage every little movement she makes toward dogdom and puppy play (she seems to need to go back to puppy play, regardless of how old she is, in order to regain that part of her life). As a shepherd, her instinct is to chase that ball. Cheer, laugh, smile, praise, reward when she does! Use all those instinctive "mothery" sounds we use when we talk to small children and animals. Show her you are pleased.
If she's afraid to put anything in her mouth, perhaps smear a little of something she likes on it-- squirty cheese, a tiny bit of peanut butter, something like that. So she is encouraged to get it near her mouth. And sometimes dogs don't care for the plastic sqeak toys-- my dog only likes the furry ones (eg-- ones disguised as slippers, bones, etc., with material and stuffing). Try a few different types.
As for the noises, she might have grown up in a household that was abusive toward others, not just her, and heard a lot of screaming and yelling that was attached to strong negative emotions-- dogs feel that, of course, and connect with it forever. The best thing you can do with noises, is try not to let the house be "silent" if you can. When you're with her, have music on in the background, even tv, etc. Keep it on low. Play with her, show her affection, play normally, calmly, it's all okay. As she is comfortable with each level of noise, slowly increase the level. Continue acting as if all is normal. If she is a bit distressed by the level of sound, lower it to the level she is happy at again for a couple more days, then increase it a bit more, very slowly. Get her used to the sound at each level and happy there before you increase it. Continue to act as all is normal, as though the noise isn't there. Eventually, gradually, when she has progressed through a lot of levels, get someone to introduce a sudden noise, like a door shutting. When that happens. Remain light-hearted, "Whoops!"-- but never comfort a dog in her unbased fear-- to a dog, that is confirmation that there's something to be nervous about. Instinct in us is to cuddle and tell the dog there's nothing to be afraid of. In dog, they look for a pack leader, an alpha dog, to SHOW them what is acceptable, what is dangerous, and what's not. You have to show by example-- if the noise isn't scary, ignore it. If the toy is to play with, do it. Praise praise praise.
You have months of work ahead of you, I won't kid you. But if you put your heart and soul into it, you will have the dog you were meant to have, and the she will be the dog she was born to be. You are doing a terrific thing. Good luck and God bless.
My own dogs, dog school, and lots of reading.