13 Day itinerary and JR pass (Tokyo-Nagoya-Takayama-Kyoto(osaka)-Osaka-Tokyo)

Your plans are very difficult because they are too long for a 7 day rail pass and your plans just don't include enough travel to cover the cost of a 14 day pass.
Also you are not including Nara at all, and missing the Todaiji Great Buddha there is like going to India and skipping the Taj Mahal. Regarding seeing the sakura - hate to say this, but every good place you can think of is going to be jammed with people - especially in Tokyo. At any rate, here are the best places in Kyoto and Tokyo:

http://www.japan-guide.com/e/e3951.html

http://www.japan-guide.com/e/e3050.html

In Kyoto, Haradani-en Garden is one lesser known place in the hills behind Kinkakuji. Since you are already going to see Tokyo, you can largely omit Osaka during the day. Nara is one great place to spend a day, as well as the newly renovated Himeji castle. It's still easy to enjoy Osaka in the evening after the Kyoto temples/shrines close down around 5PM. In fact, Dotonbori at night is a must-see place:

https://www.youtube.com/watch?v=COJ_MeXbeow

I hope the more elderly couple is in good health and ready to climb, since Fushimi Inari is mostly going uphill - you can spend some time there or the whole day if you want to romp on all the trails. But it can be tiring if you are not ready for it:

https://www.youtube.com/watch?v=EandKTAwfOM

For the Tsukiji Fish Market, numbers are very limited - 2 groups of about 60 people, and you need to be there between 4:30 AM to 5:00 AM to have any real chance of getting on a tour. Eating seems to be very important to your trip - you can see a lot of places at:

http://www.bento.com

But I wouldn't waste time trying to track down a certain restaurant unless it's something very special you want to try.

Good luck!

Hello there,

It is indeed hard to match a JR Pass to your current itinerary, however a 7 day JR Pass could work out very well if you were to return to Tokyo in the evening on the 5th, instead of the following day on the 6th. I think this is worth considering if you can manage it with your accommodation bookings. Otherwise I think buying normal rail tickets is the best option.

Takayama is also a very nice place to visit and the Hida Beef is very good! The center4 Hamburgers is a very nice visit (if you like good Hamburgers).

Kyoto will be busy with Sakura viewers, however I think this is part of the charge. Not only do you get to see the Sakura, you also experience Japanese customs around it. You'll see many people picnicking below the cherry blossom threes and you may be invited to join them, it's happened to me on several occasions. By the 6th of April, the Sakura may already be over in Kyoto/Osaka and it may be better to plan it in sooner.

For Tokyo, if you are looking for good shopping place, I think a visit to Omote-Sando makes for a great choice, you can combine it with a visit to Harajuku, Yoyogi Park, Meji Shrine and Shibuya.

If you do like food, consider a visit to Kappa-Bashi in Tokyo, selling everything food and Kitchen related.

Hope this helps,
Daniel