Perhaps the most confusing thing now is how it all fits together to make a coherent story. This is part interface, and part the confusing timelines of world creation mythos, world detailing, and beginning rudimentary story all proceeding in parallel.
Yes, this is something I am still conceptually working on. I want to have a "soft enforce" of consistency within a story, but I am not yet sure how to do that in the best way possible, thinking through some ideas (e.g. every chapter has to re-use at least one activated story element).