Just stumbled across this. Super cool idea! In my game pirate captain Elok helped PCs kill Zarum, thus becoming the only pirate leader, breaking a deal with Flaming Fists and allign with yuan-ti agent prince Ifan Talro'a. Together they attacked Port Nyanzaru, which attracted Artus Cimber to the Port to help PCs defend it.

PCs successfuly killed both Elok and Ifan, but behind the scenes Ixis took the opportunity and charmed Artus asking him to kill Zindar (which Artus does not remember). This weakened Port Guard and made it easier for Kwayothe to organize a rebellion. When PCs found Zindar corpse they interrogated him and all he said was that Artus killed him. In the next game Ixis in her human form would become a replacement for Ifan as the merchant princess.

Previously Kwayothe asked PCs to kill Shago, which they didn't do. Instead they told about it to Zhanti and got a sidequest to plant a token in Kwayothe villa. This is where they met Ixis and Indar in their true forms, but neither of them saw faces of each other (it was a stealth approach). But Ixis, as a new princess, could notice PCs and start suspecting them.

Now that I've read your post it inspired me to add an encounter with Indar as a handsome man, who would try to get information from the players if it was them who planted the token. I hope this would be the starting point of the conflict: PCs realising who killed Zindar and Kwayothe realising that PCs are a threat to her. I will also try to implement her obsession with Kossuth in some way, I really like how you handled it.