Fankly I don't care for the ship idea at all. Hunting down that interesting blacksmith, however, has flavor and could serve as a way to buff your PCs that are havng problems instead of bringing them down a notch. Perhaps he is reclusive and lives on an island in the center of the bay, what is in the water? Does he only come out at night? What if his ritual is sinister and includes more than just salt water?
Minimal old school sub, not bad. To improve I would add some details to differentiate the sub from the movie. Some ideas might be giving the villagers something other than a stash of weapons to protect, or a different motive for the bandits to be stealing their grain.
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I don't think a write up of Seven Samurai brings anything to the table that isn't put there by saying Seven Samurai, unless you were going to iron out some details, toss in some new character profiles and give some time lines for a GM to produce a fun retelling of seven samurai.
I like the idea of rallying a village to help defend it. In the TV mini-series, Pillars of the Earth (and novel, though never read it.), there is a battle of the correct scale for PCS' - the attackers are about 20 men at arms and knights attacking a small town. A small number of 'PCs' help rally the defense with a nice small scale battle.
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For a twist: The villagers knew they could not win and poisoned their grain. The bandits have taken and eaten some of it, but not before selling off a great deal to various local populations. During a time of bad harvest can the PCs manage to find and stop the shipments before they are consumed? Should they cure the bandits if they come across them dying?