Only one stop between Japan and the US? Hmm... That's a mighty long trip for a sailing vessel. You can manage it, but you're going to need a lot of salt beef, hard tack, and fresh water in the hold, and finding a spring on the island in between will be crucial.

Oh, wait, what am I thinking... this is D&D... and you probably have a cleric. Okay, you can get away with carrying fewer supplies if you can Create Food and Drink.

Are you crossing the equator during the journey? If so, you're likely to hit your campaign setting's version of the doldrums. They're not just annoying, they can be lethal if your supplies run out before you get a good wind. Magic will really come in handy here.

As for the ship... you'll either want a carrack for cargo capacity and stability in rough seas or a caravel for speed and maneuverability... which your smuggler friends would find handy for their primary occupation. You can manage either with a crew of three dozen, though a crew of that size might be a bit small for a carrack and a bit large for a caravel.

A carrack would probably weather storms a good bit better than a caravel, although both are fully capable of making it through... and fully capable of sinking en route. I hope your smugglers are good sailors.

Monster attacks at sea aren't a bad idea. D&D has a lot of fun critters you can use for that. The number one thing you need to remember about fights at sea... particularly fights this far from land... is that any battle against something that's more maneuverable in the water than your ship is a defensive action, and if your boat sinks, you're all dead. If a hole gets put in the hull below the water line... you may very well die. If you lose enough masts and/or sails to prevent you from making sufficient speed... you may very well die... slowly. If a creature of sufficient size attacks without warning from underneath the ship... you may die before you even realize you're in an encounter. You're going to have to be very careful in designing these encounters if you want to keep from TPKing your party.

Alright now... Columbus's journey was roughly 4000 miles, give or take a hundred or two, and it's 5142 miles (straight line) from San Francisco to Tokyo. This seems rather fast, but Wiki says that Columbus's little trip lasted from the August 3rd to October 12th. I'd say, then, that your voyage will take somewhere between two and three quarters and three and a quarter months, depending on conditions.

If we assume that the ship has primarily been used for coastal smuggling in the past and that monster attacks are fairly uncommon, then its arms will probably be quite light. Depending on your tech level they could have... hmm... maybe six to twelve small cannons or... probably just crossbows for the crew if you don't have cannons yet.

If you're attacked by pirates they'll be in smaller, more maneuverable, more heavily armed vessels, and they'd probably tear you apart if you didn't have PCs on board. You're certainly not likely to see them on the open sea, but the closer you are to shore the closer you are to their hunting grounds. If you tick of the wrong person and end up attacked by, say, a galleon... run away. And if running doesn't work, hope your wizard prepared a lot of fireballs.

The on-ship dungeon isn't a really good idea. No matter how valuable their cargo, rigging traps on board a ship is too risky. Besides, why would the PCs want to be getting where their smuggler friends don't want them to be going? Trying to skim a little off the top, are we?

Has any contact been made with "Hawaii" or "Japan" before by any people from "the US"? Is there any sort of trade relationship between them? If your crew is making first contact, it'll be interesting, to say the least. If there's hostile relations between the countries you could end up with the "Japanese" navy being sicced on you. If there's a formal trade relationship and your vessel isn't properly licensed for trade with "Japan," then you could end up in trouble with the "US."

And that's about all that comes to mind right now.