I'm just finishing up running this adventure for my group. I did some heavy editing of the story flow to improve transitions.
0. Linking from Skinsaw: easy enough, I had comments in Xanesha's list of targets, suggesting some names (merchants from TF and other nearby towns) be referred on to Lucrecia. (I dropped the whole Magnimar hook to TF; I never felt the connection was strong enough between the city and town/fort.)
1. Flood & Skull's Crossing: After coming to TF and finding the gambling barge sunk, and Lucrecia ostensibly dead, the PCs were at a loss. They got to meet some of the Black Arrows at the tavern; the Fort was still standing at this point. The flood came the next day. (I included Black Magga; I had no problem with them wanting to pursue her as she left-I made them suitably scared of her.) After aiding the town, the mayor asked them to investigate the dam. The town in the meantime sent runners to the Fort, asking for more post-flood help.
2. Graul Farm: The town never heard back from the Fort; the runners never returned. The PCs set out to investigate, getting sidetracked by the Graul craziness while on their way there.
3. Fort Rannick: With the aid of the freed Black Arrows, the PCs retook the Fort. In the process they uncovered Kaven's treachery and learned more backstory from him.
4. Seige: I plan to take the advice of others and have Barl's forces assault the Fort, a week after the PCs retook it. I will not let Barl spill any beans about Jorgenfist.
Then time for more down-time, allowing the PCs to enjoy their new fort. I'll let them winter there, craft items, and have them invited back to Sandpoint somehow. I like the "Goblin Day" idea in FOTSG, but waiting until next Fall? Too long.
Also, I've dropped the whole Myriana-Lamatar sidestory; it was merely an excuse/hint to go up Hook Mtn, which I've unnecessary with the seige.