All good questions. My wife and i recently bough a German Shepherd as well. He is now a 10 month old 100 lb bohemoth. Training them early is very important.
In regards to the biting a stern "no" or yelp worked for us as well. Puppys use their mouths for everything (ours still does some) it's something they will grow out of.
Ours wasnt crated for long because we had the same problem as you. I've heard of putting something in their that smells like you (a shirt, shoes, shorts) something you wouldn't mind getting chewed on. I've also hear of people covering the crate with a blanket at night so it's completely dark and also makes the dog feel more relaxed/safe. Give the puppy lots of excersise so its tired at night. If you wear them out, they will sleep better. I try to take ours on 3 walks/day and also play fetch in the yard.
Discipline is tricky. We have never used a timeout corner for a dog. A stern "no" worked pretty good for us. Teaching them commands like sit, lay down, and stay are always useful when a dog is misbehaving too.
Always socialize your dog as well. Let him play with other dogs and see other people (strangers) daily. GSD's can become aggresive. Ours began to act out on us at roughly around 5 months old, barking and growling at people, especially kids. So we set up play dates with a friend who owns a dog and also with a couple down the block who have some younger kids he can run around with. This is still something we are working on.
Exercise often and teach him commands. They are smart dogs and will catch on.
I have heard the same thing about covering the crate with a towel/blanket. I believe the person that told me that it gives them a sense of their primal instincts of being in a den? Not sure if it is true so take it for what it is worth.