Ethics: authoritarian, militaristic, spiritualist
Civics: Masterful Crafters + Warrior Culture
Species traits: Aquatic, Strong, Traditional, Unruly
The ethics should be self-explanatory. Warrior Cultures is for the samurai and Masterful Crafters is for the stereotype of Japanese honing their craft to perfection. Strong and Traditional is again to reinforce the militaristic & spiritualistic aspect. Unruly because samurai were precisely that throughout much of Japanese history. You'll have 1 point left over to spend on whatever. You could also add a 1 point bad trait and pick up Intelligent or Rapid Breeders.
And of course, this is a RP focused suggestion and I wasn't paying much attention to mechanical aspects of the choises. That said, Masterful Crafters is a very nice civic that just makes the early game smoother in a number of ways. You need to worry a little less about CG, you save some minerals, a building slot opens up on your capital a little sooner, you engineering techs are a little bit faster, you have a little bit more energy. Nothing spectacular in the long run, but it just makes everything go smoother at the start, which you can then snowball from.
Warrior Culture and Strong are a bit bad because armies aren't very important in this game, but they are very much fitting for the theme.
Spiritual + Traditional isn't normally that great because research > Unity, but for Here Be Dragons you want to get 4 ascension perks ASAP, so it's good.