Stan Hansen's autobiography has a lot of material about Japan, but mostly from the 70s and 80s. I would have loved to have read more about the 90s All Japan scene. This is a very good book and I recommend it.
I have not read it, but Lion's Pride is about the history of New Japan. I heard you probably would not learn much if you are already a fan of the product.
I thought the Ring of Hell chapter on Japan was very interesting, but like the rest of the book, it is not a pleasant read and almost makes you feel ashamed to watch wrestling.
Also, Total MMA has a nice history of the beginnings of MMA and the Japan influence, especially with UWF, Pride, etc. Great book for MMA fans.
There may be other books on Japan, but those stand out for me.