Look up Fodors member rkkwan as he just posted his honeymoon report to Japan. Congrats!

You could stay a night in Takayama, a night in Shirakawa-go and a couple of nights or more in Kanazawa. Takayama - S-go - Kanazawa is on the Nohi bus line and very easy. http://www.nouhibus.co.jp/english/shirakawago_kanazawa.html

If a JR Pass is worth it or not depends on your itinerary to the very day. You can check prices on www.hyperdia.com (use total and uncheck Nozomi) and compare pay as you go to JR Pass.

3 nights does seem a long time for Takayama.

We stayed two nights, arriving early afternoon on the first day and leaving in the morning on departure day. The reason we opted for two nights was because our stay coincided with the annual autumn festival. Even with the extra activities of the festival, the two nights gave us time to enjoy wandering the old town, meandering through the marvellous morning market (alliteration unintended and my husband took a walk along the temples path area too.

I'm not sure what we'd have done with a third day -- we'd have found something but I think two nights were plenty.

I'd definitely look at combining it with a visit to Shirakawa-go if possible.

Or you could head to Hiroshima and Miyajima. We spent a few hours in Hiroshima and then overnighted in Miyajima. I think we could easily have spent a second night on Miyajima and seen more of the island. Again, that's two nights not three, but I'd add the extra night to Kyoto or go to Koyasan.

What time does your flight arrive in Japan?

You have non-JR optioons to get from Narita Airport to Tokyo to Hakone at the beginning and don't really need a JR Pass in Tokyo at the end (unless you plan a significant day/overnight trip from Tokyo, e.g. to Nikko).

Counting day 1 as the day you leave Hakone until your return to Tokyo you would have 7 nights away from Tokyo. That means your return would be on day 8.

To make use of 7-day JR Pass, you would want to return to Tokyo on day 7. That would be easy enough to do, traveling from Takayama or Kyoto or Kanazawa or elsewhere to Tokyo in the evening/night. That is, you would have 5 nights in Tokyo at the end.

The easiest way to do it would be to return on day 7 from Kyoto. Another way is to see the sights of Takayama that day and go to Tokyo that evening.

Three nights in Takayama, two full days, is more than necessary for Takayama. A day trip (overnight would be better) from Takayama to Shirakawago would be worthwhile.

I don't think a 14-day pass would be economical. Maybe. You would be able to use it only one way between the airport and Tokyo because, with 14 nights in Japan, your trip covers 15 days.

mrwunrful-Why would an overnight in S-go be better than seeing it as a full or half day trip from either K or T? Is it to have the experience of sleeping in the farmhouse (which to me does not look all that comfortable)?

Yes on both counts.

Yes, but it is more than just sleeping. Go to experience staying at a gassho zukuri, having a meal there, the irori fireplace, a minshuku experience, and to experience S-go after the day-trippers have left and before they arrive. And, of course, to spend some time with Japanese that live in the country, like the Otani family at Koemon.

Yes, it is not as comfortable as staying in a hotel. The toilet is down the hall. Your bedding will be a futon on the floor. Furnishings in the room will be sparse. There will be a heater. And if you go in winter, Koemon (maybe others) has excellent boots that you can use and even fit my big feet.

I've expressed my enthusiasm for visitiing S-go in other threads and that is, in a large part due to my experience in staying overnight (I did not sleep well, did not like having to go down the hall for the toilet, but it was still worth it).

The other thing I love about Shirakawago is its (level of) authenticity. It is a tourist place, not truly authentic, but it is close, at least it is much closer to the real thing than the Hida no Sato museum in Takayama. People live there. The location is pretty and charming and it is the actual place where those farmhouses lived before the tourists came.

[while I am discussing authenticity I will mention that given a choice between Ginkakuji and Kinkakuji in Kyoto, I chose the former, because of its authenticity (at least parts of it have survived over centuries). G is not as photogenic as K, but the existing K is a rebuild from 1955. While I am at it, i will mention my interest in Todaiji - it is not just its beauty, impressive size, or the spirtual aspects of it that I like. It is because it is the real thing, at least parts, and been reconstructed but that was a long time ago. It is because the object that I am admiring is the one created centuries ago, and not as a tourist draw. To me, like Ginkakuji, it is a connection to the past, to the people who created it as a place of worship, and to the people who have admired it and worshipped there over time. It has that "old school" feel, spiritual to me quite apart from it being a place of worship, if that makes sense.]