The journal is being worked on and fairly complicated with so many quests/girls.
In time it will be 100% accurate. For the time being it's advised to complete quests around the day you're on and complete quests from other girls as well.
Also, about the variation with darker moments. This game has multiple paths.
You've chosen the Dark Path for Sophia so it does get dark while choosing the Good Path will be totally different and not dark at all. There are other choices that will completely alter the outcome of certain girls, the story and more.
Yea i can understand it being a complex web with this many characters. But for some it says "complete the questline up to day x for characters y and z." Thats why i mentioned it.
Yea the Sophia dark path is... damn thats so fuckin dark. I will have to give the good path a go to scrub my brain form what happened to her. Damn.