Great game, huge improvement over the last one with factions and reasonably powerful firepower upgrades. For bosses, I recommend a fully powered flame thrower with light hull, medium sails, and the rapid cannon. This combo can kill pretty much any large boss, otherwise basic cannonballs seem to be the most effective with the range boost.
Huh, a challenge for the brave, after the final boss, beat the dungeon from 1 - 99 in one go, no shopping, and must collect ALL gold chests and stat gems
you need to plan ahead of time before conquering japan. Make sure that you have vast armies of samurai, as they're the only ones who can stand up to the virus... As well as making sure that all of the good terrain is in your favor.