A few years ago, I toured Japan. I used JR 5-day Tour Pass. I travelled in overnight SinGanSan train and saved hotel bill. Usually, I went to the train station station around 10PM and do a little research and took a train around mid-night. Four to six hours later I am in another city/state. If no SinGanSan available, I also took local trains which are good too, just slower.