I adopted Chama at 5 weeks old and she did not act like this but I had a very stable gsd at the time who helped me to socialize her.
That said, I agree with the previous poster that you need to step back and rethink your approach. Fear aggression is really tricky and rarely seen in such a young puppy. It honestly sounds like you are making her fear worse and right now you should be helping to build her confidence, not take her down a notch.
There is a really great group on Yahoo for shy dogs (and fearful dogs) called Shyk9s. I would join that group and start doing a lot of reading. You want to set her up for success and keep things positive and you are going to have to start all over again with her training and your training!
Also, throw the dominance/submission stuff out the window--it's taking you down the wrong track.
Ruth & the 4 Legged Rescue Gang
Rafi the malaroo
Gio & Varda, the krazy kittens
....In my heart: