Wow, awesome! Both of those versions look great. I personally like his Shinobi 3 look a little more, but the Shinobi 2 look is always a classic. You do what you want to do!
I don't know how far you've gotten on his attacks, but you'll definitely want to give him some attacks with his knives, both for throwing and for slicing. Joe Musashi loves his knives, after all!
He uses his sword, too, but not as much as his knives.
You said you wanted to include moves from Shinobi PS2? May I suggest a stealth dash like all the characters can use in that game? It would make for a great evasion move. You could use my Hibana as reference and use the dash sound effect from her if you want. As for moves from Shinobi 3DS, his father Jiro uses a parry move in that game that blocks projectiles and allows him to do a dashing counter-attack. So you could give him that. Jiro also uses a grapple hook in that game to pull a boss toward him and slice her with his sword, so there's an attack you could use for Joe!
I've heard that Shinobi 3 music remix before. I really love it!
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