If you are on a tight deadline, its best that you take the Shinkansen. Traveling between prefectures is the one that will take most of the time.  This Seishun 18 Kippu usually applies to those who are strong enough to travel long distance, using the slow JR train.  I've checked from Hyperdia, the difference in length of time for Tokyo <--> Kyoto traveling are: Shinkansen: 2 hours ++ JR Rail: 13 hours ++   However, I'm not saying its not possible. If you know yourself that you can persevere, then this is what I advise:  See? It's a rough plan, but yeah, it's do-able.  BUT!  Assuming that you might not be fluent in Japanese language, how sure are you that you can find your way through the puzzle train lines from Tokyo - Kyoto - Tokyo? Of course, I think the train stations would have English spelling names, but still, even I might find it hard (because my sense of directions are also bad lol).  So this is why I would suggest either take the expensive Shinkansen. Or maybe just the cheap bus. Buses are cheaper than the Seishun 18 Kippu (around 4000 Yen++ per destination) but it travels as slow as the JR Rails (or maybe slightly faster... just slightly).  Using JR Rail, at those time of night travel, you might have to switch trains, which means more added confusion of trying to figure out where you are at that time LOL At least with bus, you KNOW you are going to reach your destination directly non-stop (they'll stop occasionally for their customers to buy food or go toilet). However, I dare not say more on bus because I've never taken a bus to travel long distance. The furthest bus ride I went was from Shibuya to Mt. Fuji, but that was on a tour group.

Emm..Japan domestic Flight also cheap...Most Japan people like travel by plane rather than Shinkansen.  Can you see the domestik flight from tokyo to osaka , kyoto , kansai , chitose all by flight more. Japan is the only in world domestik flight need using B747 and B777 to fly domestik...too much passenger  I at Narita i saw once very shocking time table on airport  JAL 12.30pm flight from Narita to Kansai got 4 gate....4 JAL B747 from narita flight to Kansai same time...taking 1600 people ANA 12.30pm Flight from narita to Kansai got 3 gate ...2 B777 1 B747 from narita to Kansai same time..taking 1200 people  total 2800 Japanese are fliging at 12.30 from narita to Kansai at 12.30pm........it still got 1.30 2.30 same amount.....Japan people flight like Gila!!!!