Also I have some suggestions regarding Christianity
Currently I see that there is no head of the religion and since Rome is far away from Japan I think that religion structure should be more decentralised (and similar to orthodox christianity in vanilla?) with Missionary Bishop (probably naban/portugese) being head of religion; (there would be potential to extend network of lesser bishopies if you start expanding as christian daimyo)
Also it would be cool to have possiblity to (later) declare yourself head of Japanese church.
I don't know much about history of Japan so cerrect me if something is wrong.
The grand master of the Jesuits (or his Asian representative) could be alternative to the Pope. It is historical, and would give us some unique mechanics (but again, we have a lot of things to do... XD)