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Validity of pass on trains

Hello, I am travelling with my family of 4 to Japan in August and we have a full itinerary. I have worked out it is probably best for us to buy a JR 21 day pass, based on costs calculated with Hyperdia, but have some questions:
1. In hyperdia there is often a quote for a fare and reservation. With the JR pass, is the reservation fee additional or included in the pass? Where do I reserve for trains in Japan, and can I reserve all my trains in advance?
2. I assume all train references beginning with JR in hyperdia (e.g. JR Yokosuko line to Kamakura) are covered by the JR pass. Is this correct?
3. When travelling from Tokyo to Kawaguchiko, do we need to buy supplements for the Fujikiyu Railway Ltd Exp 5 and the Ltd EXP Kaiji 101?
4. From Tokyo to Takayama do we need a supplement for the Ltd Exp Hida 7 and Ltd Exp Hida 6 to Kyoto from Takayama?
5. From Kyoto to Koyasan, do we need a supplement on the following trains: Ltd EXP Koya 5 and Nankai Koya san cable?
6. What about the Ltd EXP Haruka 16?

Many thanks.

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    Hi,
    With the JR Pass, advance seat reservations are a free perk thrown in. For a few trains like the Hayabusa, seat reservations are actually required. With JR East you can do them online, but that is the exception - the others the only way is in Japan at a JR station or office.
    For your second question, all JR lines are covered. There are a few unusual lines where you can use the JR Pass on a non-JR line (usually former JR lines) but a fee may be required. I suggest you look carefully through the official info at:
    http://www.japanrailpass.net
    It will answer nearly question that you may have.

    For Hyperdia, they don't broadcast it but basically when you look up a train route, if any trains appear as purple then it is _not_ a JR train and you'd need to pay separately for it. So you see that Fujikyu and Nankai are not covered, but the Haruka is. Another tip is to click on the "More Options" link and deselect Airplane, and Nozomi since you won't be using them with a rail pass.

    For Koyasan you should look into getting a Koyasan World Heritage Ticket:
    http://www.japan-guide.com/e/e2358_012.html
    For the Mt Fuji area there are several also, for Hakone, the Fuji 5 Lakes area or both:
    http://www.odakyu.jp/english/deels/
    http://www.japan-guide.com/e/e6905.html
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