Here are two fare finders for trains in the JP:
Welcome to Jorudan Co.,Ltd. and
www.zone81.com. Sometimes, Jorudan overestimates the total fare. The express/semi express charge for the seat in addition to the fare. These will give you fare, line changes and time tables. Always keep in mind too that trains will make it to their final destination around 11:30 and 12 where they stay for the night. They do not run again until 5 to 6 in the morning. You need to know the station name you are trying to reach which for most cities is the name of the city, but in big cities there will be more than one station. Lastly, I've never been to Kyoto so you are on your own there. I will tell you cheapest hotels are around 3000 yen and mid-range are 6 to 7000. Capsule hotels are usually the cheapest until you go somewhere like a backpackers inn and hostels. If you don't know what a capsule is, I highly reccommend the experience.