The simple answer is that you don't need to keep all the different threads in your head at the same time.
Use the player lead approach you're used to. Give the visitor's book to the players to reference and build off, then use the referee's book to surface challenges and problems as they play. The referee's book presents factions, events, and locations to provide fuel, not firm structure. You can share events between sessions and ask players to pick what they'll focus on, while rolling randomly to see what else happens in the background.
The basic idea of most OSR or OSR-ish or sandboxy games (whichever term you prefer) is to give content you then generate from randomly or semi-randomly (or even just for straight-up cherry-picking). There's no right or wrong way to play an adventure, much less a sandbox.
And best part is, if you break it, it's fine - it was made for breaking :)