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After your arrival, passport and customs clearance, head downstairs to the basement level JR stations, located in both terminals of the airport. The most convenient train is the Narita Express (N'EX), which leaves roughly every half hour for a 53-minute trip to Tokyo Station. Tickets for the entire trip up to Nagano Station can be purchased here; JR East Passes and Japan Rail Passes can also be exchanged at the JR East Travel Service Centers (see below).
At Tokyo Station, head upstairs for the Hokuriku Shinkansen (the station is always busy, but all lines are well marked—just follow the signs). Hokuriku Shinkansen trains depart from platforms 20 through 23; all trains stop at Nagano Station, so you have many choices.
The transfer from the Hokuriku Shinkansen to the local Shinano Tetsudo was recently streamlined so you can simply roll through the gate and on to the local train platform (with elevators helping you get your gear down to all platforms). The slideshows below will help show you where you need to go on both the way to and returning from Myoko.
From both Osaka or Kyoto, take the Tokaido Shinkansen to Nagoya. At Osaka, go to Shin-Osaka Station to catch the train; the trip to Nagoya will take 55 minutes. From Kyoto Station, the trip to Nagoya will take 40 minutes. At Nagoya Station, transfer to the Chuo Line for the Shinano Limited Express train to Nagano Station, a roughly three-hour trip. At Nagano, basically follow the instructions above, except that you will exit once from the local train platforms, not the Shinkansen platforms, to purchase your ticket on the Shinano Tetsudo to Myokokogen Station.