There will be a bit of variation on the terrain. There will be plenty of mountains (The Mitsumine land is very mountainous) but some areas will have long plains and the like. Instead of a Shogun, there is a ruling Emperor to the which all the clans pledge their allegiance and compete to curry his favor. I was thinking of dividing the land into around 7 or 8 great clans with smaller ones in between. Plus, perhaps animal motiffs for each of the clans, leaning with giving the Mitsumine a wolf.

As mentioned, the Mitsumine have a lot of forested mountain terrain in their territory. They possess mines from which good steel and silver are acquired, which secured wealth and weapons which have put them in prominence within the realm despite a good amount of their territory being unusable due to its wild and rough features. They are on the far north of the proposed island nation, with the only other settled landmass further north being on another island. Furthermore, given all the unsettled lands in the Mitsumine territory there is a big youkai presence within. 

On youkai and spiritual matters, they both exist, however they are somewhat in hiding. Most people can't see the smaller youkai and the big nasties live far apart from civilization that the common peasant will never see glance of them. There are people who know the truth and deal with it, but to most these are belief which go unproven all their lives or foolish superstition of the rough people in the outskirts. Youkai and Kami do take part in human life, however, as mentioned, mostly in hiding or myth. Priests actively fight and exorcise Youkai with their prayers or try to attract the favor of Kami. However, the fate of man in civilized lands tends to be settled on the open by humans. The clans fight with soldiers and steel and so does their fortunes increase or decrease... however, having supernatural help on your side is quite a boon. And the opposite... really not healthy.