You're running up against the brick wall for all families of Japanese ancestry: as far as I know, there are no reliable sources of family information beyond koseki. And the historical reach of koseki is only to the 1870s, when the Meiji government first instituted them. Before the 1868 Meiji Restoration, many families informally recorded major life events at a local temple. These temple records can take your search back earlier than the 1870s, but they are not guaranteed to exist. If they do, well, there's no central depository for them so the only way to track them down is to canvass on foot all the temples in the present-day area of your ancestors' village and hope you hit paydirt. Probably the best way to seek temple records is to make contact with distant cousins who live in the local area and ask them to do it for you, as they would know which temple to approach and they would speak the local dialect to converse with the temple staff.
In my case, I got lucky: an elderly 2nd cousin of mine whom I contacted as part of my genealogy research kindly offered to go to the local temple and retrieve what was there. He came back with a death register that listed family members' first names, their death date, age at death, and relationship to the family (e.g. daughter of X). But even this temple record stretched my tree on that line back only one more generation.
On another family branch, a distant Japanese cousin apparently traced his (and therefore, my) line back 10 generations to 1700 along the male line. (He did not document his info sources, so I presume he got his info from temple records.) His work makes clear that you can make significant headway, but it will take more legwork than merely requesting and translating a document from a gov't agency or library.
If there are other sources to consult, I've not had luck uncovering them as yet...