R Maps
[edit to add]
I haven't read the entire thread yet, others may have suggested.
However, if I was to run one of Paizo's APs, I'd go through and note every NPC, major and minor, and every faction, major and minor, and then create an R Map of the entire campaign - probably in Miro.
If I was feeling feisty, I'd probably add to each NPC and faction a list of encounters and which book and chapter the encounter appeared
Another way I might handle would be to create a spreadsheet with same info, but without the r-map visual linkage. Just the NPC name, Faction they belong to, encounter-chapter-volume