1. What's the difference between "he was gone" and "he had gone"? The former just states a past fact. The latter states it in regard to another event. eg I looked for him. He had gone.
2. Does "what are you up to?" mean "what are you doing now?"? Yes
"What are you up to?" can also mean "What misbehavior are you planning?" It can suggest that you believe the other person is doing something or is about to do something that they should not be doing.