Alright, so I'm revisiting this after a few weeks of consideration.
I'm still planning on having Seven Days to the Grave take place after the Skinsaw Murders and the Curse of the Lady's Light, linking them through Ironbriar's journals, Vorel's Phage and a redeemed Oriana who will serve as the group's 'in' into the city. The plot will be as follows:
Xanesha, having escaped the PC's in the Shadow Clock tower and having lost key minions in Ironbriar, the Scarecrow, the Skinsaw cult and her cadre of faceless stalkers decides to oversee the plans she has set in motion in Korvosa personally and relocates there. Her intent is to use the disease developed by the Red Mantis Assassins and the Urgotha Cult to kill as many people in Korvosa as possible, spreading it through the infectious silver and thereby catching as many greedy souls as possible in her sweep.
The doctors will be in her employ, moving through the city and offering a bogus treatment which will include the branding of the sihedron rune to mark someone as having been made no longer infectious which is, of course, a complete lie. The ship will have been her machinations and I'm thinking about either replacing Lady Andaisin with her as the final boss (or making the two of them lovers and being encountered together which might be too tough a final battle, I'm still weighing all of that). Some of the encounters I won't be using and a couple I'll likely add, but I really like the idea of the wererats, of them being blamed, a potential war brewing and the PC's making allies of them by stopping the war from happening. They'll become agents/spies for the characters, offering valuable clues as to what's really going on and where people can be found.
Queen Illeosa's role in all this is going to be pretty minor if any at all. My plan is to have her under Sorshien's sway, unknown to any - including herself - and for her to have had no role in the plague. In fact, its her distraction that allowed for Xanesha to infiltrate and use her plague-carriers and her false doctors to spread the disease entirely. I do plan on having her take notice of the PC's and their quest before the end of the story however, or perhaps just at the end, which is where the rival party will be established and put on the PC's trail. Sorshien also wants to reassemble the Sihedron - it was why Illeosa sent the Grey Maidens to the Lady's Light to recover the Shard of Lust in the first place. In the aftermath of the plague that infected her city, she realizes Karzoug's (or more likely some unknown Runelord rival) machinations have already begun and she moves to thwart him as well, meaning that the PC's won't receive the full attentions of Illeosa/Sorshien and that the rival party will act as a surrogate in that matter.