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Cleaning ears is more likely to prevent infections than docking them. There are sometimes legit reasons to dock ears or tails, but not often in a standard household pet.
Your pup is just that - a puppy, now separated from littermates and in a strange environment. Try crate training him, starting now (also helps with potty training), and consider wrapping a ticking clock in a light blanket or kitchen towel and leaving that with him to soothe him.
Since he is a young puppy, you are going to have to make extra effort to spend time with him and socialize him properly. Dobermans are very protective of those they are bonded with, but you have to develop that bond (and the pack order) early on. Taking him to a class is a good idea, but be certain you take the time to play with him, stimulate him, exercise him (simply setting him outside won't be enough).
Dobermans can be a higher energy breed and more intelligent breed, which requires hands on working, and ideally, giving them puzzle toys to keep them occupied. Bored dogs and unexercised dogs are the dogs most likely to get into trouble. Dogs that are kept busy, well socialized and included in their families' lives and well exercised are tired and easier to train.
