the JR night bus is comfortable as long as you don't take the Seishun Mega Dream ( the cheapest ) cause its narrow there is not much space for the legs to stretch into. But if you get the 6000yen ( $60 approx ) or the 8000yen bus its very comfortable , the chair can be reclined, you have a blanket and a slipper and there is toilet inside .. tokyo - osaka night bus takes about 6-8 hours.. usually the bus leaves around 10-11 pm and usually arrive at around 6-7 am, but you will be sleeping the whole time ..
also if you buy the ticket in advance, you get around 10% discount.. so it gets cheaper..
Osaka can actually be toured in one day, that is if you are just going to do some sightseeing. Get the one day ticket for the subway that cost 850yen. If you are touring the city on a weekday, start around 9am after the rush hour. But if you want to try the osaka subway rush hour, try starting at 8am and be prepare to be squished hehehee...
Kyoto, will I love this place and never get tired of visiting it. Anyways, the cheapest to get around Kyoto is to get the One-day ticket bus which is only 500yen, it will get you to all areas of Kyoto as long as the city bus goes there that is.. Depends on how fast you move, you can visit the major tourist destination in about a day
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Kobe and Himeji, if you don't have the JR pass, get the Hanshin one day ticket cost around 2000yen, ride all you can on Hanshin train from OSAKA to Himeji. Don't miss the Himeji Castle, its Japan's most beautiful Castle.
Hiroshima, Miyajima , Beppu , Kagoshima, Takayama, Toyama, Nara, Wakayama, Nikko, Hakone... Yamaguchi, Hagi, hehehe I could go on....
you can visit all this places using the JR pass.. and don't necessarily stay at the place , you can always go back with the shinkansen to your hotel at night.. just be sure to check the train schedule..