Here is a list of books and journal articles I have read. Updated 12th June 2014.
Book reference list (Chicago)
Bix, Herbert P. 2001. Hirohito and the making of modern Japan. New York, NY: Perennial.
Booth, Alan. 1995. Looking for the lost: journeys through a vanishing Japan. New York: Kodansha International.
Booth, Alan. 1997. The roads to Sata: a 2000-mile walk through Japan. New York: Kodansha International.
Bryant, Anthony J., and Angus McBride. 1989. The samurai. London: Osprey.
Bryant, Anthony J. 1994. Samurai, 1550-1600. London: Osprey.
Bryant, Anthony J. 1995. Sekigahara 1600: the final struggle for power. London: Osprey
Clancy, Judith. 2008. Exploring Kyoto. California: Stone Bridge Press
Clancy, Judith. 2012. Kyoto – City of Zen. HK: Tuttle
Delgado, James P. 2008. Khubilai Khan’s lost fleet: in search of a legendary armada. Berkeley: University of California Press.
Fitzhugh, William W., and Chisato O. Dubreuil. 1999. Ainu: Spirit of a Northern People. [Washington, D.C.]: Arctic Studies Center, National Museum of Natural History, Smithsonian Institution in Association with University of Washington Press.
Gerster, Robin. 2008. Travels in atomic sunshine: Australia and the occupation of Japan. Carlton North, Vic: Scribe Publications. NEW
Hanley, S. B. (1991). Tokugawa society: material culture, standard of living, and life-styles. In J. W. Hall (Ed.), The Cambridge history of Japan (660-705) Cambridge: Cambridge University Press.
Hane, Mikiso. 1991. Premodern Japan: a historical survey. Boulder: Westview Press.
Harootunian, H. D. (1995). Late Tokugawa culture and thought. In M. B. Jansen (Ed.), The Emergence of Meiji Japan (53-137). Cambridge: Cambridge University Press.
Jansen, Marius B. 1994. Sakamoto Ryōma and the Meiji restoration. New York: Columbia University Press.
Jansen, Marius B. 1995. Warrior rule in Japan. New York, Cambridge University Press.
Jansen, Marius B. 1997. The emergence of Meiji Japan. New York, Cambridge University Press.
Lamers, Jeroen P. 2000. Japonius Tyrannus: the Japanese Warlord, Oda Nobunaga reconsidered. Leiden: Hotei.
NEW Lambe, Michael & Turner, Ted. 2014. Deep Kyoto Walks. Kindle Edition.
Martin. J and Martin P. 2010. Kyoto – 29 Walks in Japan’s Ancient Capital. HK: Tuttle
Mitchelhill, Jennifer, and David Green. 2004. Castles of the samurai: power and beauty. Tokyo: Kodansha International Ltd.
Miyamoto, Musashi, Munenori Yagyū, and Thomas Cleary. 1993. The book of five rings.: Including The book of family traditions on the art of war / by Yagyū Munenori. Boston u.a: Shambhala.
Mizoguchi, Kōji. 2002. An archaeological history of Japan, 30,000 B.P. to A.D. 700. Philadelphia, Pa: University of Pennsylvania Press.
Ravina, Mark. 2004. The last samurai: the life and battles of Saigō Takamori. Hoboken, N.J.: John Wiley & Sons.
Takamure, Itsue. 2010. The 1918 Shikoku pilgrimage of Takamure Itsue: an English translation of Musume junreiki. Bowen Island, BC: Bowen Pub.
Turnbull, Stephen R. 1989. Samurai warlords: the book of the daimyō. London: Blandford.
Turnbull, Stephen R., and Howard Gerrard. 2000. Nagashino 1575. Oxford: Osprey Pub.
Turnbull, Stephen R. 2001. Ashigaru 1467-1649: weapons, armour, tactics. Oxford: Osprey Military.
Turnbull, Stephen R., and Peter Dennis. 2003. Japanese castles, 1540-1640. Oxford: Osprey Pub.
Turnbull, Stephen R., and Wayne Reynolds. 2003. Fighting ships of the Far East. 2, Japan and Korea AD 612-1639. Oxford: Osprey.
Turnbull, Stephen R. 2009. The samurai capture a king: Okinawa, 1609. Oxford: Osprey
Turnbull, Stephen R., and Richard Hook. 2010. The Mongol invasions of Japan, 1274 and 1281. Oxford: Osprey Pub.
Tsang, Carol Richmond. 2007. War and faith: Ikkō ikki in late Muromachi Japan. Cambridge, Mass: Harvard University Asia Center.
Sadler, A. L. 2009. Shogun: the life of Tokugawa Ieyasu. Tokyo: Tuttle Pub.
Shiba, Ryōtarō, and Juliet Winters Carpenter. 2004. The last shogun: the life of Tokugawa Yoshinobu. New York: Kodansha International
Souyri, Pierre-François. 2001. The world turned upside down: medieval Japanese society. New York: Columbia University Press.
Walker, Brett L. 2001. The conquest of Ainu lands: ecology and culture in Japanese expansion, 1590-1800. Berkeley: University of California Press.
Yoshikawa, Eiji. 1981. Musashi. New York, N.Y.: Harper & Row/Kodansha International.
Yoshikawa, Eiji, and William Scott Wilson. 2000. Taiko an epic novel of war and glory in feudal Japan. Tokyo: Kodansha International.
There are thousands of journal articles relating to Japanese history. The ones I have listed here are only the articles I have read for my own interest or research. If you need any help finding a journal article I am more than happy to help you.
Ambaras, David R. 1998. “Social Knowledge, Cultural Capital, and the New Middle Class in Japan, 1895-1912”. The Journal of Japanese Studies. 24 (1): 1.
Boxer, C. R. (1951). The Christian century in Japan: 1549-1650. Berkeley: University of California Press.
Breen, John. 1996. “The Imperial Oath of April 1868: Ritual, Politics, and Power in the Restoration”. Monumenta Nipponica. 51 (4): 407-429
Cavendish, R. (2001) St Francis Xavier departs from Japan: November 21st, 1551, History Today; Nov, No. 51, Academic Research Library
Chor, So Wai. 2002. “The Making of the Guomindang’s Japan Policy, 1932-1937: The Roles of Chiang Kai-Shek and Wang Jingwei”. Modern China. 28 (2): 213-252.
Corr, William. 1997. “Tokugawa Ieyasu’s Englishman”. Japan Quarterly. 44 (1): 74.
Craig, Albert. 1959. “The Restoration Movement in Chōshū”. The Journal of Asian Studies. 18 (2): 187-197.
Delgado, James P. 2003. “Relics of the Kamikaze – Excavations off Japan’s coast are uncovering Kublai Khan’s ill-fated invasion fleet”. Archaeology. 56 (1): 36.
Garon, Sheldon M. 1986. “State and Religion in Imperial Japan, 1912-1945”. Journal of Japanese Studies. 12 (2): 273-302.
“The Licheng Rebellion of 1941: Class, Gender, and Leadership in the Sino-Japanese War”. 1997. Modern China. 23 (2): 216-245.
Goodman, David S. G. 1994. “JinJiLuYu in the Sino-Japanese War: The Border Region and the Border Region Government”. The China Quarterly. 140.
Harrison, Simon. 2006. “Skull trophies of the Pacific War: transgressive objects of remembrance”. Journal of the Royal Anthropological Institute. 12 (4): 817-836.
Innes, Robert, and Ronald P. Toby. 1985. “State and Diplomacy in Early Modern Japan: Asia in the Development of the Tokugawa Bakufu”. The Journal of Asian Studies. 44 (2): 408.
Kazui, Tashiro, and Susan Downing Videen. 1982. “Foreign Relations during the Edo Period: Sakoku Reexamined”. Journal of Japanese Studies. 8 (2): 283-306.
Kidder, J. Edward. 1990. “Saddle Bows and Rump Plumes. More on the Fujinoki Tomb”. Monumenta Nipponica. 45 (1): 75-85.
Kidder, J. Edward. 1987. “The Fujinoki Tomb and Its Grave-Goods”. Monumenta Nipponica. 42 (1): 57-87.
Kidder, J. Edward. 1972. “The Newly Discovered Takamatsuzuka Tomb”. Monumenta Nipponica. 27 (3): 245-251.
Nosco, Peter. 2007. “The Experiences of Christians during the Underground Years and Thereafter”. Japanese Journal of Religious Studies. 34 (1): 85-97.
Nosco, P. (1993) Secrecy and the Transmission of Tradition, Issues in the Study of the “Underground” Christians. Japanese Journal of Religious Studies, 20/1
Ohnuki-Tierney, Emiko. 1976. “Regional variations in Ainu culture”. American Ethnologist : Journal of the American Anthropological Association. 3 (2): 297-329.
Pitelka, Morgan. 2009. “The Empire of Things: Tokugawa Ieyasu’s Material Legacy and Cultural Profile”. Japanese Studies. 29 (1): 19-32.
Sevela, M. 1998. “Sakhalin: The Japanese Under Soviet Rule”. HISTORY TODAY. 48: 41-46.
Sheldon, C. D. (1983). Merchants and society in Tokugawa Japan. Modern Asian Studies. Vol. 4(3), 477-488.
Stavros, Matthew. 2009. “Locational Pedigree and Warrior Status in Medieval Kyoto: The Residences of Ashikaga Yoshimitsu”. Japanese Studies. 29 (1): 3-18.
Steele, M. William. 1981. “Against the Restoration. Katsu Kaishu’s Attempt to Reinstate the Tokugawa Family”. Monumenta Nipponica. 36 (3): 299-316.
Tashiro, K., and Videen, S. D. (1982). Foreign relations during the Edo period: Sasoku re-examined. Journal of Japanese studies. Vol. 8(2) 283-306.
Toby, R. P. (1977). Reopening the question of sakoku: Diplomacy in the legitimation of the Tokugawa Bakufu. Journal of Japanese studies. Vol. 3(2) 323-363.
White, J. W. (1988). State growth and popular protest in Tokugawa Japan. Journal of Japanese studies. Vol. 14(1) 1-25
Williams, M. (2009) [Review of the book Ideology and Christianity in Japan, by Kiri Paramore]. Chicago Journals, Vol. 114, No. 5, pp. 1427-1428
Yates, Charles L. 1994. “Saigō Takamori in the Emergence of Meiji Japan”. Modern Asian Studies. 28 (3): 449-474.
Yonetani, Julia. 2000. “Ambiguous Traces and the Politics of Sameness: Placing Okinawa in Meiji Japan”. Japanese Studies. 20 (1/1): 15.