I have mentioned this many times, and if you had already seen it, I am sorry. However, you can see video segments about Japanese history on the NHK高校講座 page. http://www.nhk.or.jp/kokokoza/library/2 … index.html
I've read real books about it (some referenced on Wikipedia) and while a lot of Japanese people has helped with the research in those books, all of em were written in English.
I would guess it's much easier to find fictional books about it in japanese since English is the language of science, but I guess that depends on your level of ambition, there's probably a lot of "simpler" books about it in Japanese.
If you did want English, then The Coming of the Barbarians is a popular-history treatment of the early years of foreign settlement (based on diaries, letters and so on). It's slightly pre-Meiji but I liked it enough that I figured I'd mention it here anyway.