I don't know if everyone has had the problem but this adventure is supposed to raise your PCs(assuming 4-5) to 7th level by the end. I don't see that happening, even with a total cleanup of all of the encounters and no NPC aid.
Since some foes will escape and certain NPCs are bound to be involved in certain combats, I see something like 17,000-18,000 experience(plus bonuses) as the likely result.
The answer would appear to be the wandering monsters which have a 28% chance per day while hugging the coast, reduced to 8% per day on the open seas. However, ignoring the risks of random dice either denying you your wanderers or, alternately, drowning your players in random foes, I just don't like the feel of too many such events.
After all, if there are that many regular problems, why would the trade route be viable?
Instead I feel that the number should be limited to 150% of the experience you feel is likely to be needed to reach 7th level and should make a certain degree of sense.
Further, as the PCs are facing monsters on the open sea, treasure is going to be something of an issue.
I'll be back tomorrow with a few ideas I had on this but eagerly await any comments or advice on the matter.