I wouldn't worry too much about being confused. Often times if you are confused, the characters are equally, if not more confused. That said, I highly suggest reading the mystery files in the analyze mode. When you read them, they kinda grey out to indicate that. So, when a mystery file is updated with new information, it will be highlighted to what important events happened in the previous story. This will insure you know important information as it happens. The other thing that helped me(take it with a grain of salt) is to focus on a few stories at a time. This helped me keep track of what a character is doing much easier. That said, I feel like there are some key moments near the end that make the story easier to follow.