I think the Samurai should stay the 1st UU of Japan. I mean, it's one of the most iconic UU in the game.
I did consider using the Zero as the 2nd Japanese UU. But what use does it has in the game? None. It will never be used. It's a waste to use it as a UU. Especially if it's the vanilla UU.
I wouldn't use the Shiro as the vanilla UB of Japan. I'm afraid it's obselete before you can even think of building it. However, you can always make it obselete with a later tech.
The Jinja is a good UB. (That's why I use it as a 2nd UB

)
But personally, I don't have much problems with the Kaizen Plant actually. If you apply the changes I suggested in post 418, it's an attractable building to have.