I have actually been thinking about this for a long while, and decided it might help to write down all my thoughts on this conversion both for feedback, sharing, and perhaps extra ideas.
The core of the idea is rebuilding the Kingmaker campaign to revolve not around Nyrissa, but rather the intrigue between the three ancient wyrms of the region: Choral, Ilthuliak, and Silverstep. (Personally, I feel that Silverstep is more than likely a translation/transliteration or nickname, but that's neither here nor there, since the party would pretty much only deal with him through his daughter, Eranex.) There's already more than enough elements of the draconic to make this conversion quite simple, especially with Nyrissa's weak connection to the campaign's plot early on, and I don't plan on tossing her completely, just downgrading her to Ilthuliak's ally/lieutenant/consort. (I personally like the last option best, but can understand it having 'squicky' implications to others.)
To this end, several changes would be made throughout the story to better integrate this conflict into the story and foreshadow things better.
To begin with, I would replace the mites in book 1 with a second tribe of black-scaled kobolds, turning the conflict into a holy crusade, with the new tribe worshiping an effigy of Ilthuliak herself, still certain that their patron will once again turn her eye to the Narlmarches and reward their loyalty. The Stag Lord, meanwhile, is a distraction to keep Brevoy's eyes on the Greenbelt rather than the River Kingdom of Pitax, where Ilthuliak is staging a coup to claim the city as her own in the guise of Adrienna Irovetti. His alcoholism stems from the realization that he's just a pawn of Nyrissa, that his men are nothing but bandits and thugs, and his dreams of founding a new River Kingdom in the Greenbelt will never come to fruition. To this end, definitely play up the angle of Happs collecting 'taxes', and make it obvious that the bandits are all wearing uniforms, and the silver medallions could even be similar to the seals of office carried by Brevoy's magistrates.
While Nyrissa's ploy with the Stag Lord did indeed keep attention away from events in Pitax, in book 2 there are now several new settlements being founded in the Stolen Lands, and this is clearly a threat to Ilthuliak's longterm plans at a time when she's far too busy consolidating power in Pitax to deal with the upstarts without showing herself, which would tip her hand too early. As a wyrm, she could decimate all four nations with ease, but then Brevoy would be ready for her, hiring dragonslayers from across the Inner Sea to deal with the threat on their doorstep. To this end, Nyrissa sends one of her allies to spur a local troll into uniting the trolls of the southern Greenbelt into a unified force that will slow expansion and perhaps even destroy the upstarts. There's also the possibility that the trolls will find Briar, which Nyrissa is still searching for, but Nyrissa quickly turns her focus to recruiting more allies, including barbarian tribes from the north. The biggest change here, aside from adding in components like Hargulka's Monster Kingdom, is to make Candlemere into an ancient wizard's tower sitting atop a cyclopean tomb. The wizard is long dead, slain by the cyclops wight whose tomb the wizard had been slowly excavating. This should help foreshadow Vordakai a bit better, and get the party interested in the history of the region, with murals on the walls of the tomb depicting events of the years since Earthfall with uncanny accuracy, and seeming to depict events that have not yet even come to pass.
Books three and four will be swapped, allowing Vordakai to be a full-powered lich, and with the tournament moved forward from book 5 so that the party encounters 'Irovetti' early on. In this case, however, the tournament serves to get Drelev out of the way, and so that Ilthuliak can size up the players personally, now that Nyrissa's plots have failed spectacularly twice. For the most part, this means rebalancing a lot of encounters in the Hooktongue Slough for a lower level party.
In the revamped Varnhold Vanishing, puzzle pieces start faling together as the party encounters Eranex, who is working to find Briar before Nyrissa can, and discovers a big hint to the secret behind The Vanishing of Brevoy's royal house a decade earlier. It becomes clear that someone acquired a large number of soul jars just like Vordakai's, and that the Rogarvias may still be 'alive', trapped in soul jars somewhere. The truth is that Ilthuliak had acquired dozens of the magical items from archaeological digs throughout the region over the centuries, and used them all at once to capture every living descendant of her rival, Choral. Choral went into hiding in the Golushkins, seizing hold of the dwarven holdfast there, and has spent the intervening years trying to discover who was responsible while keeping Brevoy's political situation destabilized so that he can reclaim the throne once he's ready to enact revenge. Vordakai's actions alert Choral's spy network, and the players will have to deal with an adult red dragon showing up to claim Vordakai's lair just as soon as they defeat the ancient lich and begin freeing the townfolk of Varnhold.
Book 5 no longer needs the tournament at the start, since the players will already be distracted by events far to the east and trying to puzzle out being attacked by a red dragon. Seemingly overnight, everything will fall apart, as Choral's machinations cause Brevoy to descend into civil war just as Ilthuliak, in her guise of Duchess Adrienna Irovetti, launches a surprise attack on the party's kingdom. No help will be coming from Restov, and indeed they will likely beg the party for help even as marauders invade the western half of the players' kingdom. Neither Ilthuliak nor Choral will show themselves directly at this point though, and confronting Irovetti should result in a scene similar to Ming the Merciless in Flash Gordon, as she retreats to Nyrissa's pocket realm of Thousandbreaths, leaving Briar behind in her secondary lair in Pitax.
Book 6 should be especially filled with additional intrigue, as it becomes clear that there's more that two factions in the Brevic Civil War, and Choral tries to court favor with the players in order to get them to help track down the fled Ilthuliak and Nyrissa so that he can focus on winning the war in Brevoy, while Eranex tries to get the party to turn Briar over to her for safekeeping rather than use it against Nyrissa and Ilthuliak. Ultimately, this can play out many different ways, but Choral appearing just as Nyrissa and Ilthuliak are slain, then attacking the party in fury at being denied the pleasure of killing his rival by puny humans is certainly a good option.
So, thoughts? Input? Critique?