My impression of Clavell's work (I enjoyed Shōgun, but it's not a patch on Tai-Pan IMO) has always been that he does his research pretty meticulously. Clavell served in the British army in Malaya during the Second World War, and was a Japanese prisoner of war in Singapore and Indonesia, so he's got at least some lived experience when it comes to the cultures and societies of the Far East.

Your question is a really interesting one, because it touches on a broader intellectual question about how Western writers (of fiction, history, whatever) understand Japan and the Far East, and how they represent that culture and society in their work. The risk, obviously, is that they slide into Orientalism and fetishisation or caricature.

Curiously enough, a group of American academics (from a mix of Japanese history/Asian Studies disciplines) actually produced a volume of essays in the 1980s entitled Learning from Shōgun: Japanese History and Western Fantasy, which you can read online. I think you'd find it really interesting by way of a detailed, quite granular answer to your question.

The first essay in the book — James Clavell and the Legend of the British Samurai by Henry Smith — is on the Blackthorne character, and his historical basis (William Adams) — it's a pretty comprehensive summary of what we know about Adams, and his time in Japan. Its essential point is that the 'English samurai' myth is somewhat overblown:

Did he become a samurai? If by “samurai” we mean a bushi, a member of the warrior class, then the answer must certainly be no, Adams never became a samurai. It is true that he was provided an estate by Ieyasu, for whom he thereby became a retainer. It is also true, according to the account of the chief of the English trading station, that he left two swords—the customary mark of samurai status—to his son Joseph at his death. Yet in no surviving records has any hint of military interest or prowess been ascribed to Adams. He remained a dedicated man of commerce—a calling which was anathema to the bushi class.

Adams’ status can be more persuasively explained as akin to doctors, scholars, priests, artists, and others of essentially professional or advisory function. [pp. 6-7]

I think you'd also find Ronald Toby's essay Trade and Diplomacy in the Era of Shōgun [pp. 43-51] instructive as regards your question about interactions between the Japanese and Europeans.

The general tone of the essays is pretty positive — the overarching narrative is about Shōgun as a popular cultural reference point for Japanese history and society, and the role of literature in fostering cross-cultural understanding. The authors seem to give Clavell a lot of leeway for artistic license — which I think is reasonable, when dealing with historical fiction — while suggesting that his overall approach is fairly culturally/socially sensitive and broadly historically accurate. Here's an extract from Elgin Heinz's piece, Shōgun as an Introduction to Cross-Cultural Learning:

Because of its romantic elements, some academic historians dismiss Shōgun as false both to the real circumstances in Japan and to the character of William Adams. Clavell does not bother to refute them. He subtitled his book “A Novel of Japan” and invented new names for those characters that can be identified with historical figures. Thus, he felt justified in making them behave according to the logic of his theme instead of according to the frequently tedious and sometimes mystifying accounts of written chronicles. Would anyone deny that the struggle for power is clarified by telescoping several interacting governing bodies into a single Council of Regents?

Other historians, more lenient, note that many of the novel’s apparent anachronisms are acceptable, given its pivotal time frame. Enormous changes took place in Japan within a single lifetime centered around the year 1600. Who can tell precisely when a particu- lar phenomenon began or ended? An English historian, Hugh Ross Williamson, writing on the whole problem of taking liberties with the “facts” of history, argues plausibly that all of academic history is a “combination of myth, propaganda, and guesswork . . . . Even when the writer has grasped the fact that history is the interaction of character and not the invention and propagation of myths, . . . he cannot invent speeches and thoughts for his people; he can only record what he can prove.” The historical novelist, on the other hand, like the great Greek dramatists, working With known outcomes, can interpret the facts so that “an aspect of truth emerges which should compel the audience’s belief” (Historical Whodunits [1956], pp. 12-22). [p.29]

Source: Henry Smith, ed., Learning from Shogun: Japanese History and Western Fantasy (University of California Santa Barbara, 1980).

Edit: typos.

K1990 answer is the best...but as someone who's read the book thirteen times and then looked into the history of Japan at that time...much of the cultural information is relatively accurate to written reports of customs at the time.

Sure the 'Novel' is still a novel...but it's Historical Fiction. The setting is very accurate, the character analogs a bit less so for artistic license.

I learned much about Courtesan culture that I later found to be completely accurate. The way they first created 'red light district' style brothels. The history of the Mama-sans, etc. That they measured time in 'sticks' of incense. That Imperial Courtiers blackened their teeth. Bunches of interesting tidbits I was unaware of previously.

I have not finished the book. But I do recall people being a little more seppuku happy than they were in reality. Not that it did not happen, but people seemed to be offing themselves like every other page, or talking about offing themselves, which I don't think was quite accurate. Seppuku was most common as an alternative to execution by the state or capture in battle. It did happen for other reasons as well, (death of a lord for example) but not everyone was chomping at the bit to kill themselves over every little dishonor