Following the walkthrough, I had a total of 11 people including my main character, flintlock pistols for all 11, and did 50 stat points in VIT and the rest in DEX to provide massive damage and accuracy. In addition, I gave all of my units the "Sniper Shot" skill I bought from a town store. It looks to be a regular skill book, but possibly at higher-level towns.
As a result of this book, and with setting my units to the upper-right portion of the ship, I could reach every enemy on an opposing boat without moving. And with high DEX over a hundred or more, each shot was generally a one-hit kill. I didn't have to board; just wait for the enemies to die, then press
to scrap the enemy ship.
With this possible, I simply navigated to as many high-level enemy ships as I could find, going to islands only when I needed to reveal more of the map. With the sniper skill, those islands got cleared as well.