By which line will you come to Tokyo Station? Or, will it be the first station on the way?
Tokyo Station building is huge. There are two Shinkansen zones of JR-East and of JR-Central.
JR-East is using a green JR icon.
In signs for Shinkansen in Tokyo Station, Tohoku Shinkansen is mentioned first among JR-East Shinkansen lines, as in "Tohoku, Yamagata, Akita, Joetsu, Nagano Shinkansen."
JR-Central is using an orange JR icon, and is operating Tokaido Shinkansen (Tokyo -- Shin-Osaka).
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http://www.japanrailpass.net/In this page you see JR icons of the six JR passenger railway companies.
[From Tokyo to Hiroshima by Shinkansen]
When will you travel to Hiroshima?
(It is announced that on 10 November 2013, Tokaido and San'yo Shinkansen trains will be delayed after 8:30 in the morning.)
then transfer to another JR Shinkansen Hikari train to Hiroshima. Your second Shinkansen train may also be a Sakura....
No gate exists between Tokaido Shinkansen (of JR-Central) and San'yo Shinkansen (of JR-West) in Shin-Osaka Sta.
(These two JR companies are using the one Shinkansen zone in Shin-Osaka Sta.)
So, there basically you would not have your pass checked at a gate by an attendant (unless you look like trying to get outside the Shinkansen zone).
In Shin-Osaka Sta., Shinkansen tracks are on the 3rd floor, and a Shinkansen concourse is on the 2nd floor; you can use elevators to change platforms.
If your second Shinkansen train departs at Track 20 in Shin-Osaka, you will change elevators on the middle floor, from the one connecting the concourse and Track 21 & 22 platform to the other connecting the middle floor and Track 20 platform.
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http://www.jr-odekake.net/eki/img/premises/0610155.pdfIn Hiroshima Sta., the easiest way to get from the Shinkansen zone (for Tracks 11 through 14) to South Exit (near a bus terminal and a streetcar stop) is to pass through a Shinkansen transfer gate (saying you hope to reach South Exit), cross a bridge over non-Shinkansen tracks and pass through South exiting gate. If you have reserved your Shinkansen seat, the seat ticket(s) would be collected at the first gate for you to use.
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http://www.jr-odekake.net/eki/img/premises/0800613.pdf[From Tokyo to Nikko by JR-East lines]
Please note that only a small numbers of trains are available to get from/to Utsunomiya to/from Nikko by JR-East.
Depending on combinations of Shinkansen and Nikko Line trains, you will have much time to wait in Utsunomiya Station.
Utsunomiya Station is simple and small. If you have reserved your Shinkansen seat, the seat ticket would be collected at a Shinkansen transfer gate when you pass through it for Nikko Line.
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http://www.jreast.co.jp/e/stations/e248.html