When your flights are fixed, check which terminal of which airport each flight is going to use in Japan.
And, if you leave Japan from Narita Airport, consider using 7-day JR Passes, as Uji-san suggests.
This pass may pay off even if you activate it after reaching Tokyo Disney Resort.
http://www.japanrailpass.net/eng/en001.htmlFor this will be your first visit to Japan, I try to suggest routes on which I guess you would change trains easily.
Sometimes the cases are in which it appears easy to change trains on a route map but indeed it takes long time and/or distance.
e.g.
Tokyo: JR trains from / for Narita Airport, JR trains from / for Maihama (near Tokyo Disney Resort), each use platforms deep underground. Changes between these JR trains and other JR trains on upper floors (including Shinkansen trains) take long.
Asakusa: Stations of Tobu, on subway Ginza Line, on subway Toei Asakusa Line are located in this order. A change between Tobu and Toei takes long.
- Tokyo Subway Route Map
http://www.tokyometro.jp/global/en/service/pdf/routemap...
Routes with World Heritage Pass of Tobu
NRT to Nikko:
1,160 yen per adult + World Heritage Pass; Est. about 4 - 5 hours
Narita Airport Sta. / Airport Terminal 2 Sta. of Keisei
| Fare: 1,000 yen per adult;
| Ltd. Express; About 75 min.
Keisei Ueno Sta.
| Walk; About 15 min.
Ueno Sta. (G16) on subway Ginza Line: Track 2
| Fare: 160 yen per adult;
| About 5 min.
Asakusa Sta. (G19) on subway Ginza Line
| Walk; About 10 min.
Asakusa Sta. of Tobu
| Isesaki Line and Nikko Line
Tobu Nikko Sta.
Nikko to Maihama (except on weekdays):
World Heritage Pass + 400 yen per adult ; Est. about 3 - 4 hours
(The same way back to Ueno Sta. (G16) on Ginza Line)
Tobu Nikko Sta.
| Nikko Line and Isesaki Line
Asakusa Sta. of Tobu
| Walk; About 10 min.
Asakusa Sta. (G19) on subway Ginza Line
| Fare: 190 yen per adult to Hatchobori Sta. (H11);
| About 5 min.
Ueno Sta. (G16) on subway Ginza Line
| Walk; About 10 min.
Ueno Sta. (H17) on subway Hibiya Line: Track 1
| Train for Nakameguro; About 10 min.
Hatchobori Sta. (H11) on subway Hibiya Line
| Walk; About 10 min.
Hatchobori Sta. of JR-East
| Fare: 210 yen per adult
| Rapid or Local train for Soga; Around 15 min.
Maihama Sta.
From Maihama Sta. you can either walk or take a train of Disney Resort Line (a loop line by monorail) to get to TDL / TDS.
It is often the case with railroad routes, I think, that the cheapest one isn't the shortest one, so it's hard to meet your request "shortest and cheapest."
As to Nikko, I guess that's not so far from Tokyo to recommend Shinkansen. But, as to Kyoto from Tokyo, the cheapest route without Shinkansen takes longer and longer time.
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