Check out Dead By Dawn from the WOTC web page. Its one of the Chaos Scar adventures. I had a blast with that one. It did regulate activities within the party while the bulk of the adventurers fought zombies. "Help help.. they're getting in!" Essentially, the players were trying to hold a zombie horde out of the temple they were in.

In your case, you want them to achieve a certain list of successes? i.e. take the wheel so you can steer the boat.

That sounds more like a list of goals they need to achieve. Board, battle.. take control.. rescue. If this is just one big long session doing that linearly with them would hardly be noticed. It would be more like a movie. i.e. "You realize that you are getting further from your boat, if you don't take the wheel, she's lost." Now you have combat being directed by actual goals, which will add to the urgency. It also allows all the player to contribute to that goal.

In many respects you could have a list of things they need to do and when, and if they haven't hit your Q on time, then direct them as I described above.

The thing that I noticed was fun with Dead by Dawn was the sudden sense of urgency when the zombies broke through. The thing I disliked about it, was that it was essentially the same skill challenge each time. i.e. the same goals each time.

From what you're describing they have to;
1) Board
2) battle some big dudes
3) Gain Control of the vessel (rear deck with the wheel)
4) Hold back a swarm of skeletons
5) Seal the gates letting the skeletons out
6) Rescue Crew and Cargo

I'd almost leave the whole time line urgency requirement out. They will have their hands full as it is, and frankly boats don't move that fast.

Looking forward to reading the bat-rep and seeing the pics