Hey Arvid, I found the same problem. What helped was to simply apply the principles used in play to prep. Follow what Vx tells you to do. He tells you that this is the way to MC this game. All the elements of prep you mention are helpful, if not vital to MCing the game as intended. Instead of prioritising, perhaps just sit down with a pen and paper and follow the chapter step by step? It really does help to do so.
I kept drawing analogies to what I was doing in a traditional game which was hindering my ability to 'see' what the concept and execution of AW prep (or story games prep in general) was meant to look like. You are simply writing down cues for what to think about and which moves to make in play, depending on what the players do. They are possible RESPONSES.
So, make sure you have a scarcity / want / threat sheet on hand during play, or just some paper will do. There is no one right way to note your prep and details down, but you do need some fictionally generated relationship 'map' hooks to hang your questions on.
When you jot down notes about NPCs, do what the rules say. NAME them. Give them a want/desire and a body part they follow around in response to their need. Attach them if you can to two PC's (for conflicting reasons). Always encourage imbalance and scarcity. Re-incorporate these NPCs until dead, inconsequential or they become part of the special NPC Hx move. Write any stakes questions that you have next to these NPC triangles. Drive play to answer these questions.
I found the most helpful part of the prep chapter for me was to 'Characterise' all the elements in the game: NPC's, locations, environments. Make them WANT something from the PC's. Imagine if the players did nothing about these identified threats in the fiction? What Badness and misery would their world barf forth? Therein lie your countdowns. Make note of that, and tell the characters during play as you announce future badness.
You are a fan of the characters yeah? Don't make their lives boring yeah? Well make their adversity so 'pushy' that they have to sit up and take notice. Doing nothing (from the players perspective) causes all sorts of future badness to tick down the countdown.
Whenever you have a question about the PC's and their evolving story, ask questions about it during play, but during prep, think NPCs and their situations. If you care enough, make it a stake. Design custom moves that push toward the resolution of that question in play. Push hard on those triangles that circle around the question.
When trying to come up threats for fronts, If they haven't already been mentioned in play, I hold off. I may daydream a little in the broadest terms, and if possible ask myself a stakes question about the introduction of said threat to the situation. I really have been enjoying the embracing of 'emergent play'. So, as the front and its threats get exposed during play I can 'hang' all the prep cues on fictionally generated coolness from the table, rather than my own ideas on what the fronts / threats should be.
Hope that helps?