First time itinerary in Spring

Hello everyone!

I will be traveling to Japan for the first time in the first weeks of April/2019 for approx. 14 days, and would really appreciate some help with the itinerary! :)
I'm feeling very lost trying to figure out the railway system and the best way to get from one city to the other.

This is what I have at the moment:
Day 1-4: Tokyo, with 1 day trip to Nikko
Day 5: Matsumoto
Day 6: Kanazawa
Day 7: Shirakawa-go
Day 8: Takayama
Day 9-13: Kyoto, with 1 day trip to Nara
Day 14: Back to Tokyo

Does this itinerary make sense?
I could extend the trip to 16 days, as I still don't have the airplane tickets. I would also really like to include Hakone. And maybe Kamakura? Am I missing any unmissable places for a first trip to Japan? Any side trips from Tokyo or Kyoto which are really worthwhile? I don't really have much interest in going to Osaka or Hiroshima, though.
And, finally, would it be a good idea to purchase a JR Pass? Maybe a 7 day pass which I would activate when leaving Tokyo?

Thank you so much in advance!

Most of your questions can be answered by looking at this itinerary, removing the Hiroshima, Himeji trip & adding those days in to where you want to spend more time https://www.japan-guide.com/e/e2400_best.html

Great, thank you so much!

Thinking about it I would probably miss Matsumoto & replace it with a day trip from Tokyo to Kamakura. I would also probably buy the JR Pass for convenience.