Wow these are some great ideas. I'm just going to tweak the fighter’s skills abet for the Samurai and then have the player choose bonus feats based upon a clans style of fighting.
All of my players are going to have some sort of bonded/legacy item that grows with them as they level or achieve rp events. My last experience with buying and selling magic items in a game was not fun.
I think I'm going to leave the Shugenja class alone for the most part. I'm just going to drop the elemental focus ability for two domains one of which has to be of their chosen element. I will then divvy up the other domains by clan values ie.. Scorpion Trickery, Lion Glory.
Set I really like your Domains, Scalykind will work great for my Naga and Yaun Ti. The metal one is nice as well since I'm considering turning the crab clan into a dwarven clan.