A few random thoughts follow:
The concept that really drives Brown's formula is a system of interlocking schemes and secrets. Canon FSN and FZ both have those as a large part of their architecture as well.
The Matous? They've (kinda) got a secret Grail. Also, Zouken's been worm-raping Sakura as part of his Evil Plot To Get The Grail. Shinji did the same, except with a different motive. A lot of this emerges as part of FSN's exposition, and could easily form part of the mystery there.
The Einzberns? They screwed up BIG TIME in War #3 with Avenger. Now they've shoved a homunculus lesser Grail into the War, and she's connected to Shirou's past. Unraveling her story -- and later, the schemes that produced Avenger -- takes up a lot of FSN. Ilya's and Shirou's situation also raises lots of questions about family, connections between parents and children, etc., so you've got some potential higher-concept fodder in there as well.
The Tohsakas? Well, Tokiomi weaved a lot of schemes into Grail War #4, none of which would have been apparent to a narrator limited to non-Tohsaka viewpoints. Tokiomi's approach to that War helped spawn Kirei. And doomed Sakura, (eventually) killed Aoi, turned Rin into a broken ball of depression, and a couple others. The mess that the Tohsakas made out of War #4 is something that a character could really dig into.
Kirei? Where to begin...? The guy has plans-within-plans-within-plans. He's also kept numerous secrets for a decade -- secrets that influenced all of the characters' lives. A hidden Servant. Orphans in the basement. The fire that shaped Shirou's personality. Rin's upbringing. Avenger's identity. Aoi getting strangled. And Nasu/Urobuchi wrapped them all in a philosophical question: what do you do when your personality and desires clash with what society expects of you?
So one potentially helpful first step for developing a mystery / hook: remember Grail Wars basically consist of seven or more and schemes colliding. And that the desire to hatch each scheme usually emerges from some individual's inner drives. Those drives can often be rephrased in universal terms (magus-ey duty vs. love of family for Tokiomi, the self vs. society for Kirei and Shirou, the way that winning became its own goal for the Einzberns, the dimensions of parent/child relationships for the Kiritsugu-Ilya-Shirou mess, the darker, parasitic sides of family life for the Matous, etc.)
The second step is to figure out how the character tried to satisfy his/her drives, either in the past or present. Usually through gaming the system and cheating. But cheating the system rarely works out as planned -- Avenger emerged from that process, and it's the canonical mystery of both FZ and FSN.
You don't need all of this, but it might kickstart something.