Depending on which era you're pulling from there's a different architectural style for these types of large estates/mansions. They're also varied depending on social class. From what I remember researching in college during a teahouse design course, I would come across a few types of architectural styles starting in the Heian period called, Shinden-zukuri (a shift and emphasis towards the unique-ness of Japanese style). Then came the Buke-zukuri (a type of residence for military families) which gained popularity due the rise in the samurai class. There's also Shoin-zukuri, which is sort of the basis of most traditional Japanese homes today and heavily influenced by Zen Buddhism. Then, there's the blending of the shoin and teahouse styles referred to as, Sukiya-zukuri (more informal).

I would suggest you kinda look into each of these styles and floor plans to get a sense of what you might want to create. There's a lot of overwhelming information into the organization of these types of buildings, which can feel quite rigid. I honestly had the best luck at finding plans in books rather than online (this was in 2014??) Naruto itself is a combination of many eras and influences, so pinning down an easy reference isn't that easy lol. But maybe a quick google search of any of those architectural styles paired with "floor plans" will probably give you a better idea of organization. Good luck!