For longer distances you will have to pay more. From Tokyo to Kyoto it is around 14000 yen, one way. Finding accommodation for the night for 3500-5500 is considered a burgeon in Tokyo and is not easy to find. Unless you have special arrangements as a student of some school or you commit for a long period to some guesthouse you may find that you will have to pay much more to have a place to sleep. That is why prior arrangements are almost essentials.
Japan is a fascinating country with a lot of knowledge and beauty to offer.
Please have a lot of good and fruitful time there.