Alright, restructure everything in here so that it flows better. Some of what I’m about to post is speculative, considering I’m referencing Japanese pre-history.

The land we call Japan see its first inhabitants around 10K BCE, with the arrival of the Jomon people. They come to Japan via what was probably still connected by land in their period (unknown > S China > Taiwan > Okinawa > Kyushu). We don’t know too much about their culture or language, but there are some theories that today’s Ainu people of northern Japan are their genealogical descendants. But why distinguish them from the rest of the Japanese?

Because the true ancestor to Japanese culture and genetic structure as we know it didn’t show up until about 300 BCE, with the arrival of the Yayoi (unknown origin, but it’s believed that they came via Korea). Now, the key difference here is that whereas the Jomon people were hunter-gatherers, the Yayoi built rice-cultivating societies. So, just like with any other people anywhere else in the world during this time, bonds and societies are determined by family and marriage. This is, in essence, a clan (Japanese: umi or omi). Each umi was independent from another, and had its own umikami (lit. clan god/spirit). Due to good weather, and considering the north was still more dominated by the nomadic and semi-sedentary Ainu, the Yayoi stayed mostly in the southern part of Japan (Kyusu, Shikoku, S Honshu).

Eventually, one of the umi, the Yamato, rose over the others and became the main source of power in the isles (eventually receiving legitimacy as a state from the Emperor of China). Now, remember how every clan had an umikami? The Yamato did too, and there’s was called Amaterasu, the Sun Goddess. Like in other cultures, the Yamato subdued other peoples, and largely left them alone so long as they paid tribute, and accepted that the conqueror’s gods were stronger than their own. This is why, today, Amaterasu is the chief kami (deity/spirit) of the Shinto religion, and is considered the ancestor of the Emperor (supposedly the Yamato family is the oldest unbroken dynasty in the world).

Other than that, I’m not sure I can answer your last two questions too well. I suppose they worked and did what any other clan system did. If you’re familiar with Crusader Kings II, you know that over time certain landed elite accumulate land, and exhort power over their populace. In Japan, for example, tax was paid in rice (nom nom). Eventually you have umi playing court and military politics and manipulating the Emperor.

Court umi that controlled the Emperor did so by marrying their daughters to the Emperor. From what we understand, the Emepror idn’t have terribly much to do with raising his children, and that role was left to his wife, who’d then perpetuate the cycle by raising the child (and future Emperor) to be quite amicable with her maiden family. Such umi were the Soga (530s–645), the Fujiwara (850s–1070), the Taira (1159-1180s)

Then the military umi are the more popular shoguns we know today (Note: As you’ll see, there’s family names, then there’s period names. The period is named after the city from which the shogun was running things. In doing so, he kept the two governments, civil and military, separate, disabling the Emperor from regaining power as opposed to his puppet position). We have the Minamoto (Kamakura period, 1192-1333), the Ahikaga (Muromachi period, 1336-1573), and the Tokugawa (Edo period, 1603-1868).

Aaand, I think that's all I've got. Any more questions? Lemme know. :p

EDIT: The word for clan is uji, not umi.