4E Version comments...
Overall, I like the story a lot. Specifically, I like the way it's divided up into three distinct parts that provide ample stopping points.
What's the purpose of the scene descriptors? While in some cases they're informative (especially regarding how long each scene takes), in many cases they seem entirely superfluous. Why does a scene where the PCs talk to other PCs have a level, when there's no skill challenge or combat? Why does it need to be indicated combat takes place on a round-by-round basis?
"The Sabotage" seems rather clunky in it's presentation, and it seems like a bear to run as the first real encounter. If I'm reading it right, the idea was to have the PCs and enemies basically tug-of-war for control of the "clock." I don't really like the mechanics though. For one thing, I think the action economy for the PCs to counter is far too steep. It's much better tactically for the PCs to focus on killing enemies, and then deal with the countdown. Of course, barring enemy action, one PC can effectively stop the countdown by shoveling. It does provide an interesting tactical quandary (increased power versus countering the countdown). However, the downside is one player basically shovels while the others combat. Overall, it's a neat idea that I don't think will really work in practice (but I may be wrong).
Personally, I would (and will, eventually) run the combat straight up while giving the enemies a couple of goals (throw the amber rod, break the wards/valves, etc). Afterwards, I would probably make it a skill challenge/straight puzzle (probably with timer) for the PCs to figure out how to stop the ship from exploding. The DC/possibilities would change depending on how many rounds the PCs spent in combat and what goals the enemies accomplished.
I like tying the use of the Golden Icons to Action Points; it's an elegant way to have an "artifact" that isn't overly powerful.
I like the "Hold the Lighthouse" skill challenge (and the single page description is awesome). However, I feel the adventure has a dearth of combat encounters in it, so I'd probably run this as a straight up combat.
Clever use of my least favorite magical item: the immurement.
How many squares specifically are on fire in "The Labyrinth?" Being extremely generous, I count 7 squares, and so straight off the bat Gillie takes 35 damage. That's almost a third of his hit points right there, before he even gets to act. Being less generous, it's more like 10 squares/50 damage; almost half his hit points. Gillie won't spend any time engaging the PCs. He'll be lucky to last four rounds. I'd get rid of his mechanic altogether, and make the burning hedges deal extra damage to the PCs. The hedge disappears if Gillie is killed or convinced to stand down.
I'm glad the lower level stats for Asrabey et al were included. The higher level stats make Asrabey, for all intents and purposes, unbeatable (which may be the intention). I think the lower level version provides a much more interesting and satisfying combat while representing Asrabey as tired, but still a bad-ass. The PCs can go toe-to-toe with him and still feel heroic without actually subduing him. He still doesn't go down easily, but it's not wholly contingent on a lucky PC roll.