First off.... YES... Include the Takayama Festival, and no, I have not been to it...yet.
http://www.japan-guide.com/e/e5909.htmlThis will be the hardest thing to book, and I would suggest that you start trying to book your hotel NOW! And don't give up, there will be cancellations from time to time, and you can grab one of these, if you are persistent.
You have the ability to move things around in your schedule a lot. For instance, you start and end in Tokyo. You can do some things at the beginning, and some things at the end of your trip. This gives you some flexibility as to when you are at different places in Japan. I would do a few things in Tokyo at the beginning, say Nikko, and then jump to Kyoto to begin with.
Since you want to see cherry blossoms, and the cherry blossom season will be at the beginning of your trip, there are a few places in Tokyo that I would go to before going to Kyoto. The Dankazura in Kamakura is worth seeing.
http://www.japan-guide.com/e/e3102.htmlYou will also want to see the great Buddha in Kamakura, but my favorite Temple is Hasedara, and it's view of the ocean.
http://www.japan-guide.com/e/e3100.htmlhttp://www.japan-guide.com/e/e3101.htmlIt will not be necessary to have a JR Pass in Tokyo, but there are some nice day passes that might help.
After a few days in Tokyo, jump to Kyoto, or Osaka. This can be done with a discount train ticket, a bus, or discount airline. There is currently a Peach Air flight from Tokyo Narita (NRT) to Kansai International (KIX) on the evening of April 8th for 4090 yen.
http://www.japan-guide.com/e/e2364.htmlIt will now be peak season for Cherry blossoms, and Osaka and Kyoto will be a good place to view them. I did mention Yoshino, but since it is in the mountains at a higher elevation, go to places in Osaka and Kyoto first, and then go to Yoshino before heading to Takayama.
As I mentioned earlier, you might want to take a bus to Takayama. The Niho private bus line is based in Takayama, and has highway busses to many places. Reservation can be made here:
https://www.nouhibus.co.jp/english/highwaybus/You can also book bus tours of Shirakawa-go, and a highway bus to Kanazawa, which you also wanted to visit.
Once again, all or most of the beginning of this trip does not need a JR Pass. Going around Tokyo, Kyoto, and Osaka does not require a JR Pass. Transportation to and from Mount Koya is on private trains, and is not covered by a JR Pass.
Once you are ready to leave Kanazawa is when you will start to need the JR Pass. The two other "most scenic places in Japan" are Amanohashidate and Matsushima bay. The first is near Kyoto, and the second is near Tokyo. More links:
http://www.japan-guide.com/e/e3990.htmlhttp://www.japan-guide.com/e/e5100.htmlIf you start at Kanazawa with a JR Pass, you could hit Amanohashidate, Himeji, and Hiroshima before heading back to Tokyo. IIf you plan to stay two days in Hiroshima, I would spend an entire day at Miyajima Island, and one the other day, split your time between Peace park, and Kawachi Fuji Gardens. You would then go back to Tokyo, and do a day trip to Matsushima before the 7 day JR Pass expired. Then hit the Fuji fives lakes before heading home. Once again, getting to the Fuji five Lakes area involves private railways, and your JR Pass helps a little.
And for others who are reading, I know about the JR Limited Express train form Shinjuku, but I believe that since it uses private tracks to get to the Fuji five lakes area. A JR Pass holder will have to pay a surcharge fee.
This is a rough suggestion for how I would do this trip. I have not given exact dates, but a general plan for you to follow. I would suggest that you look at the link to the Nohi bus line, and see if you want to do more there.
