Sorry for the late response and thanks for your hints.
@Adoke: yes, there is a pirate involved, no hook, but an eye patch :-) (it's a NPC already given in the module and I used him as the mate who could also direct the PCs in case they didn't have any idea).
Here's what I did (also thanks to the help of a friendly GM):
1) Choose obstacles like sandbank, cliff, direction of wind changes, mixing it with some "open water" obstacles which gives the PCs time to prepare spells, discuss, pray ...
2) Then I divided every obstacle (and free card) into 4 fields
3) Every round (which is longer than a normal PF round of course) they advance a number of fields. I chose a base speed of 2 fields for the ship and 3 for the crocodile. Obstacles like algae would further reduce their speed by 1, sandbank would strand them completely.
4) For every obstacle I thought of 1 or 2 possible ways to solve it: for the calm they could either hoist more sails which required a climb check to go up the mast and an acrobatics check for not falling down when releasing the hawser or start rowing where they got the assistance of the sailors and required a strength check.
5) If they did well (let's say they could only release one sail), they got a +1 for the advancement, if they did very good (like: all rowing characters succeeded in their check) they got a +2.
For the skill checks: most were Str and Dex based, that's something I couldn't change. But there is also Perception where I allowed them to see 1 field per 5 points. Effectively allowing them to check what's ahead of them. Besides giving them Int checks if they didn't know what to do.
The result: This design kept it open enough to give the PCs a number of possible ways to get away: The wizard was able to cast some spells (like gust of wind) while being on open water, the cleric could try to reach his deity by praying (this is an option I sometime give the PCs in situations where they can't do much else and can grant them a circumstance bonus on insight, perception: the better the roleplaying, the lower the DC).
And my gamers liked it very much and did well (one of the gamers had ranks in Profession (Sailor) for real and came up with her own ideas on how to avoid some obstables).