Hi there,
Lets take a look at your approximate costs for your long distance travel from Tokyo that will be covered by JR:
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Tokyo > Takayama: ¥14,600 (275mins, 532km)
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Takayama > Kanazawa: ¥4,380 (186mins, 148km)
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Kanazawa > Jr-namba: ¥7,240 (182mins, 280km)
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Jr-namba > Kyoto: ¥2,880 (52mins, 55km)
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Kyoto > Jr-namba: ¥890 (55mins, 55km)
JR ticket cost: ¥29,990 for 5 legs
You'll make a small saving or break even with the JR Pass vs purchasing standard tickets within the 7 day period of long distance travel (assuming you visit Kyoto within this 7 day period too). There are other less tangible benefits to a JR Pass, such as less hassle at stations and flexibility to visit anywhere (eg, a day trip to Hiroshima from Osaka normally costing ¥20,000 return would be free). In your situation I think I'd got with the 7 day rail pass for this period for peace of mind, however whether these benefits fit your mode of travel very much depends on you.
Regarding the rest of your trip, I have the following recommendations:
Narita into Tokyo + Tokyo travel.
For the start of your trip if you think you will be mostly touring around Tokyo I recommend one of the following options from Narita:
-
metro pass with the Keisei Skyliner to get you into Tokyo from Narita on the Keisei Skyliner train inclusive of 1 or 2 days unlimited travel on the Tokyo Metro.
- [Narita Express + Suica metro prepaid card] deal. This is similar in terms of cost, but rather than some days of full metro cover gives you ¥1500 of Metro and JR travel which can be used however you like. Travel into Tokyo is covered on the slightly slower Narita Express rather than the Keisei Skyliner train. You can also use the Suica card to purchase food from convenience stores.
You can also purchase extra 1 or 2 day metro passes at Narita. The 2 day passes are great if you want to put a cap on metro travel for the family as they work out at ¥490/person/day. As a regular ticket will be somewhere between ¥160-¥190 per trip, if you do 4 metro trips per day (highly likely if sightseeing) then you'll make your money back.
Please note that these special priced combination offers and 1-2 day passes are only available for purchase at the Narita Airport Railway/Bus Ticket Counter so it's best to purchase on arrival rather than wait till you are in town.
For Shirakawago
JR doesn't run a service to Shirakawago. I recommend you use the [Nohi bus service from Takayama] to get to and from the village.
Hope this helps!