It you use JR Pass, JR East Pass or Kanto Area Pass right after you arrive in Narita, you don’t need to purchase any more deals or passes. But some of you stay in Tokyo for the first several days and activate JR Pass or other deals. In this case, you might think about additional deal for the transfer to Tokyo from Narita.
I had a trip to Tohoku area and Nagano area in this past January and February. I stayed there for only three nights. But fortunately I have got many trains, like Overnight Limited Express Akebono, Skyliner, Resort Shirakami, Fuji Kyuko, Ueda Railway, Limited Express Hakutaka. This following list is what I wanted to do in this trip:
Try to book and take overnight train on arrival day. I wanted to check how long we spend to change the pass, book and transfer to Ueno/Tokyo.
To take Resort Shirakami and Akita Nairiku Jukan Railway. I wanted to see some spots and trains in Tohoku area.
To go to Kawaguchiko (Lake Kawaguchi) station from Shinjuku via Fuji Kyuko Railway. I wanted to take both Fujisan Limited Express and Fuji Tozan Densha on Fuji Kyuko Railway.
To take a train between Nagano and Naoetsu. This section will be transferred to non JR lines in 2015. Because it will be transferred to third sector companies, Shinano Railway and Echigo Tokimeki Railway after Hokuriku Shinkansen will open. JR Pass will not cover this section.
To take Limited Express Hakutaka. This express train will be discontinued after Hokuriku Shinkansen will open in 2015.