I decided to do it the simplest and closest to the rules way: the longboat is lost :D. That's not much of a deal and was a fun event.
Just for information (and in case it gives an idea to others), I'm tracking the crew with blank cards filled with their information: it's easier (and more fun/visual) to manage them, to group them by specialities depending on the events and regroup skill checks (like all the guys with soldier + ammo, or put doctors cards on the top of the guys they are trying to heal, etc.). I've uploaded a picture on bgg, waiting for moderation now.
Also doing something I find convenient for random crew selection by throwing 1D20 + 1D6. If the D6 does 6 I choose the target, else I trust the D20 or rethrow if it's invalid. Counting the position based on the way the cards are currently aligned on the table.
I think a digital version would be a killer. It would streamline all the book keeping and would let the player entirely focus on events and choices. If I was still young with free time I would propose to try, but that's not the case so I'll just hope someones does it one day... :D.