ATM's in Japan have closing times..sometimes as early at 9:00p.m. Also, not all of them take foreign cards. So bring cash, the Japanese have not caught the plastic money craze.
See the island of Shikoku for a rural Japanese experience. Secluded, crowd free, traditional, and beautiful it is off the beaten path and often forgotten..it shoudn't be.
Visit the sacred mountain of Koya-san south of Osaka for a taste of old Japan while staying in a Buddist temple. Ethereal, beautiful experience.