INTERNAL: One example of internal conflict in To Kill a Mockingbird is man vs himself. In the story Scout must overcome her prejudice and understand empathy. She is taught by Atticus that you have to be able to walk in somebody else's shoes to understand their position.
The past perfect refers to a time earlier than before now. It is used to make it clear that one event happened before another in the past. It does not matter which event is mentioned first - the tense makes it clear which one happened first.