Although Japan Rail Pass is very attractive price for foreign tourists but if you want to travel cheaper and save the accommodation cost, the best way is to take night buses in Japan. On the other hand, buses running the day time are limited. For example, there are many night buses running between Tokyo and Kyoto but only few buses running during the day.
Then these buses are equipped with toilets which you can use them anytime and mostly are 3 seats in a row. Which means stranger will be not sitting next to you. Also, many of the buses also have AC power sockets at each seats and free WiFi.
The bad thing is that the announcements will be only in Japanese and drivers will not able to speak English. This can be curious when the buses make stops at the rest areas on the highways and there is no published time table, which means you have to listen the announcements from the drivers carefully.
Please note that JR buses operate these night buses too but Japan Rail Pass holders cannot use them without buying the tickets. However, Tokyo-Kyoto can be JPY 5000/one way, which means it can be cheaper than you accommodation cost in Tokyo.