I'll throw out a few of the tweaks I've made to the NPCs and their relationships:
Triel and Kyron were romantically involved. Kyron is the estranged nephew of Severem Navalant, whose father was murdered (by Vhalantru) so that Severem could inherit (Severem is much more tractable.) Kyron graduated from Bluecrater and left the city, returning a few years later to the region with a new name (Bonesworn,) a new girlfriend (Triel,) at the head of the Necrocants to reclaim his birthright in the name of Nerull. Drakthar was Kyron's creation, and that success is what inspired Tarkilar to try to achieve the same thing upon himself, with disastrous results. After Triel's execution, Kyron will recover her body and she will next appear as a wight at the head of an army of zombies when the PCs go to Liduton.
Alurad is one of the three missing priests of Pelor. Two of them were put into the spellweaver stasis tubes to keep them undetectable and un-rezzable, but Alurad the paladin was broken by torture and now thinks he's Adimarchus, and wears a magical neck shackle that blocks all divination.
I added an entire chapter for Liduton, a Yuan-Ti ruin centuries older than Redgorge. Access requires a golden disk (the Scale) and a key that will be on Kyron's corpse. Inside, the story of how the Yuan-Ti and the demons contested for dominance of region unfolds in hieroglyphs, and the party will make it past traps to find a mummy lord Yuan-Ti guarding an artifact stolen from the demons. The snakes thought it was destined for their use because it is a great stone egg, but were never able to bend it to their will. The party will be able to destroy it, releasing a boss made by applying the shadow dragon template to a high CR fire elemental and changing its type to fiend. Destroying the mummy guardian, the artifact, and the demon shadow fire thing will lift the curse on Liduton. The curse resulted from Kozamogon trying to harness the power of the demon shadow egg, much as the Yuan-Ti had tried centuries before, but with her greater power came more devastating effects when she failed.
Meerthan was using the identity of Elethor Ashstaff before chapter 1, survived the assassination attempt and switched identities to Tyro. Owen Marsh, innkeeper of the Lucky Monkey, is a cleric of Ffarlagn (sp?) and the real leader of the Striders, and is rez'd after Flood Season. Fario and Fellian begin recruiting NPC rangers to deal with the threats that the PCs leave behind, like gnolls near the demonscar and goblins that fled the slaughter carried out by my merry band of murder-hobos. They are highly effective and earn the respect of the party.
Maavu becomes the leader of the Chisel when Foreman steps down. After the Test of the Smoking Eye, the party goes to Redgorge to lift the siege, and is not having much success with diplomacy. Nidrama appears with much showmanship and announces that the demons, under their new ambitious general, are coming to destroy Redgorge. That brings almost everyone together and ends the bickering. For the demons' attack on Redgorge I "borrowed" heavily from "The Temple Between" in Dungeon #161, including using the maps for the challenges. Basically, the battle serves as backdrop for a number of encounters and challenges for the party to overcome, which ultimately determine the outcome of the larger conflict.
Jil grew up as a street urchin in Sasserine, she's never known her real name or her exact age. Her only friend was a half-orc youth who died at the hands of Nulin ("Fish") to save Jil from a fate worse than death. Jil, intrigued by the party, takes on a new identity as Jaklyn, wins an annual footrace sponsored by the Church of Kord, and gets a job as a tavern wench at the Drunken Morkoth, the PCs base of operations. She becomes romantically involved with a PC (cleric of Pelor.) The information broker NPC was folded into her character. The kidnap and torture of the Strider did not become murder both because of the unknowing influence of the good party member and because she discovered that the Last Laugh took the job from Fish. At that point, her goal in life becomes to kill Fish, and she will work with the party (if they let her) to achieve that goal in any way she can. She maintains a network of informants in the city, mostly beggars and the impoverished children, whom she helps in memory of her slain half-orc friend.
Nidrama and Adimarchus are siblings. Nidrama is limited to helping the PCs against the demons of the scar as an angel, which is why she casts off her immortality and "falls," becoming an Aasimar paladin and a cohort for the party. Her goal is to save Adimarchus, which requires killing him in Skullrot, then using the connection between him and a PC with the madness background feat to siphon off his immortality (possible with the cooperation of the smoking eye template person) while Admiarchus is lying in state on Occipitus. As a mortal, a greater restoration or a wish can get his head together, curing the madness that afflicted him. I determined that madness came from his exposure to the Far Realm when he was tasked with closing a portal (see "The Gates of Firestorm Peak") as an angel. This connects the "dream haunted" background feat to the Great Old One pact for the party's warlock, by the way. Afterwards, Adimarchus will "walk the Oerth" in a quest for redemption as an Aasimar favored soul, to be met in future campaigns.
"Hooknose" is female, and under the identity of Lady Taliraxia is a great patron of the arts in Cauldron. She is an unabashed hedonist. She woke up from her recent "nap" (of several decades) to find "her city" controlled by the beholder, and she's just started to work at regaining control of its criminal underground and nobility from Vhalantru. When demodands begin to rain from the sky, she takes wing and incinerates many of them, and commands the PCs to stop the cagewrights from destroying what's rightfully hers, or else she will kill them all and lay waste to the region before moving on to somewhere she can resume her decadent lifestyle. Afterwards, not content to rule behind the scenes, she declares herself monarch and demands tribute from the survivors. The party encounters her at the Demonscar Ball, the Cusp of Sunrise, at a "patronage dinner" at Vhalantru's estate after Ch. 2, and wherever else they might encounter art aficionados, hedonists, and nobility. Of course, she has items to block divination.
I have many more, but that's what was off the top of my head.