this is a great website for researching train options in Japan.
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i recently took the bullet train from Hiroshima to Tokyo, then the Narita Express to NRT, instead of waking up at 3 am to fly coach on ANA (biz class was sold out) . it was awesome, rode the bullet train for 5 hours and enjoyed every minute, and i guarantee i'd be the first to get lost. there's always someone around who speaks English and can point the way.