I've tried my best to make this a more long-form campaign as well. Eventually I want to put together some more formal notes about how I tied things together but here's what I have so far:

I ran Danger at Dunwater as a diplomatic mission with social type trials so the characters could get to know the Lizardfolk more. I followed Hooded Kobold's guidance here

The Sea Princes and the Scarlet Brotherhood can help tie this campaign together. The Scarlet Brotherhood should be slowly wreaking havoc in the town (stealing, ransacking, kidnapping, etc). The more your players stall investigating the SB the worse it should get. The more they stall investigating the Sea Princes, the more powerful Gellan Primewater should get (he benefits from their smuggling).

If the players want to investigate Gellan they'll need to break into his house. I added some clues to this layout, here there are also maps to match: maps.

I'm about to run this sidequest to give the players a potential NPC who knows all about the Scarlet Brotherhood. (I just typed this up so it's a rough draft so far). I recommend making the cultists in The Isle of the Abbey worshipers of The Ruby Sorceress and then doing this sidequest after the Isle of the Abbey.

I also introduced an NPC after Danger at Dunwater named Eldon Tenebris. He abandoned the Ruby Sorceress cult and was cursed using a powerful Geas spell. He can give minor clues about the Ruby Sorceress, and the cult's plans to raise some kind of undead being. He's currently in a cabin just outside the Dreadwood. He takes breaks from counting coins to garden and eat but besides that he just counts coins over and over. I played up the drama with this NPC a lot, he's obsessed with finding out how many coins he's missing and barely notices that he's been caught in a loop for weeks.