I recommend using a program like Evernote for organizing your work. It helps you organize a bunch of notes using tags etc. it loads and switches between documents fast which is good when dealing with a large amount of notes. As for organizing the narrative I think you should at the center have some kind of unifying theme - something that ties all the story-lines, events, scenarios, character developments, world developments together. E.g. lots of things happens in the Lord of the Rings - bunch of different races, power-struggles, various battles, various disputes between characters and groups of people, but at the center is the ring that symbolizes this dynamic of unity / domination, it's about uniting against evil. Tolkien didn't put all that complicated stuff (multiple races etc) for random world-building reasons, they served a purpose for the narrative.
Your Baccano! quote suggest you are looking for a theme that is more open-ended, but you'll still have some kind of theme. What is the game about? Where does it take place? What can the player do? What can't the player do? What paths can the player take and how does the player progress? Think about your choices and preferences and how they might tie into some kind of theme.
The more open-ended your theme is the less you actually need to organize your story-lines and scenarios. E.g. if it's about "power-struggle" then you can just let the game mechanics of the game tell the story - different factions battling, different ways to influence factions, to gain power, etc. You don't care so much which event takes place in what order, the direction things are going, just how they influence the power-dynamic. In that case you just need to have certain parameters in place for a certain event/story-line to be triggered, e.g. if faction X controls castle Y and you are from faction Z then you can do story-line C which on completion changes the parameters and potentially opens up for new story-lines.