How I should read this with the proper historical perspective? I understand the book is both strongly praised and heavily criticized, and in some cases both by the same source. What do I need to know about modern, text-contemporary and historical Japan in order to use the book best and avoid developing misconceptions?
Ruth Benedict did not speak or read Japanese and never visited Japan in her life. She researched and wrote her book during WWII, to explain the other side, based on interviews with Japanese-Americans and Japanese POWs. These facts don't completely disqualify her book, which has, as you mention, a very mixed reputation, but they're obvious handicaps to research.
She's the great popularizer of a lot of ideas about Japanese history and culture that we all almost unconsciously hold today. For example, Benedict's the one who came up with the concept of Japan as a "shame culture" as opposed to America's "guilt culture" ie. people in Japan are motivated by shame and the fear of ostracism from society, rather than by guilt and fear of punishment.
I can't condemn her work entirely, because a lot of very well-respected people find something of value to it, but I personally think that a lot of the big conclusions she made are exactly the assumptions of an honour-driven, unique, unchanging, and homogenous Japan that we need to re-examine to seriously grapple with Japanese history.
This may just be more confusing but there's a very good overview of the entire history of criticism/defence of The Sword and the Chrysanthemum: the essay Chrysanthemum’s Strange Life: Ruth Benedict in Postwar Japan by Sonia Ryang.