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Musashi was all about getting in his opponent's head, and getting them to act emotionally, thus throwing them off their game. It's more or less explicitly stated out in the Book of Five Rings (which reminds, I haven't read that this week, time to go find my book!). A duel, and indeed, any combat, is about disrupting your opponent if you are to win. A fight to the death is just that, it's war, and the goal in martial science is to win. Honor has no place in a fight to the death.
That said, as much as I love Iaijutsu Strike and the Sword Saint, it's better suited to Kenshin builds of Samurai X/Ruroni Kenshin fame. I take it whenever I play a samurai (usually) just so I can get rid of the damn mount.
Personally, I'm partial to the above idea of refluffing a Thug rogue with a Lore Warden fighter. Sneak Attack is right up Musashi's alley.
Edit: With two weapon fighting, Katana - Wakizashi. His style was all about learning to use the katana in a single hand, and the wakizashi in the other (longsword and shortsword), as that provided the most flexible method of fighting. He also proposed that all followers of the martial science (IE: War) to know how to use all of the weapons of their trade, but shouldn't specialize in any but the sword. Each weapon has their place on a battlefield, depending on where that battlefield is. One can spend their lives mastering naginata (spear/polearm) combat, and find that it is useless in a hallway or other tight confined space. One can master the shortsword for quick and precise strikes, and find themselves downed by an arrow or bullet out on a field. So, it is good to know how each weapon functions, in a sense.
Which is more or less a moot point in Pathfinder, given the extremely odd existence of hallways that are wide enough for two men to walk side by side shoulder to shoulder, no matter where you are.