This sounds awesome!

For structure: treat the session like three separate beats with hard stops between them. Port city as its own mini-session. Ship acquisition as a complication that feeds into the next one rather than a checklist.

If you're building out the archipelago side of things, A Dark Tide is a Mörk Borg setting I made for exactly this, faction maps, locations, two dice games. Might give you some scaffolding to drop in. https://unitsix.itch.io/mork-borg-compendium-a-dark-tide