You might stitch something playable together (an island hopping campaign):
Book 2 - Second Darkness: Children of the Void place island in the shackles. Replace Drow with Serpentfolk.
Book 3: Kingmaker: Varnhold Vanishing (Change Varnhold to an island colony, change Vordekai to a Serpentfolk Lich). Play up the Roanoke links and give PCs control of Varnhold as a reward at the end, and Vordekai's tomb should have a map to Savith Yhi, and hint at untold plunder!
Book 4-6: Serpent's Skull 2nd half. Play up pirates vs ninjas (red mantis) with Pathfinders and Aspis as unaligned factions. Place the city on an uncharted island in the Shackles.
Talking with my group yesterday, it seems we are going with this route. I am definitely going to crib Children of the Void. I will also consider using VV as I have heard really good things about it.
I am sofar torn on the idea to put the final city on an island or in the Sargavan mainland, but I suppose I can decide for sure a bit down the road after my player decide whether they want to buckle more swashes or do hardcore jungle exploration.
I like the pirates/ninjas idea, and I know at least two of my players love the Mantis as an organization so they will enjoy seeing them highlighted.
I will post some more plans when I have solidified some of them to try and get some more good feedback.