The Shepherd is a fantastic character, exquisitely designed, and the plot carries real intensity.
Regarding the submission, I checked my augmented CBR+PNK set and remebered that the pamphlets include a built-in progress track system for each objective. Since you have the space, I’d recommend using it. It would make tracking “the mess” the players create easier at the table.
Given how central the Shepherd is to the story, I would also consider treating him as a Hunter, complete with stats and skills. Additionally, a few concrete guidelines on how the players can help Kes would be very useful, especially for GMs who may struggle to improvise.
Finally, a couple of points could use clarification: Kes is spending what her father left her, not her husband’s. Also, it’s not immediately clear whether she works for the clinic and later joins the cult, or if the clinic itself is the cult.
Overall, a strong and compelling submission that would benefit from a bit more mechanical and narrative details.