I'd show you how to save on transport.
Day 1 - Tokyo (arriving at Narita Airport in the evening)Buy a 'Suica and NEX' package for 3,500 yen.
http://www.jreast.co.jp/e/suica-nex/index.htmlhttp://www.japan-guide.com/e/e2359_002.htmlA NEX ride ticket, 1,500 yen worth, takes you to any station in Tokyo and some surrounding areas.
Day 2 - TokyoUse the 1,500 yen suica credit to get around Tokyo. If you can't complete it, buy some food and drinks at the designated shops, and get a refund of suica card (500 yen).
Day 3 - Tokyo to Osaka (Sinkansen)Queue up for the non-reserved seat section of the Nozomi train at Tokyo Station, where nearly all the Osaka bound Shinkansen originate. Therefore you can definitely get a seat.
Nozomi runs 4 to 8 times an hour and takes 156 minutes to Shin-Osaka.
Tokyo to Shin-Osaka: 13,240 yen (non-reserved)
810 yen more in a reserved seat.
Day 4 - Visiting Kyoto from OsakaTake the Hankyu Kyoto Line limited express from Osaka Umeda to Kyoto Kawaramachi. It runs every 10 minutes, takes 43 minutes and costs 390 yen each way.
Day 5 - Visiting Kyoto and Kobe from OsakaTo get to Kobe Sannomiya, take the Hankyu Kobe Line limited express. It runs every 10 minutes, takes 27 minutes and costs 310 yen each way.
Day 6 - OsakaIf you take the subway and the bus a lot, buy a one day unlimited travel pass for 850 yen.
Day 7 - Leaving Japan via Osaka Kansai AirportTake the limousine bus from Umeda. It runs every 20 minutes, costs 1,300 yen each way and takes 50 minutes.