best travel route japan

Hello! would love to get some advice
We will be in Japan for about 3 weeks. What would be the best route using the JR pass?

Arriving in Tokyo and we would like to explore the following
1.Tokyo
2.Snow monkey -Nagano area
3. Kawazu - early blooming cherry blossom (we will need to be here around end of Feb -early March)
4. Kyoto
5.possible Kyushu to see authentic samurai making

Thanks
Star

i wonder:
* why you wanna go especially kawazu (there are many places where cherry blooms, and especially if you intend to go south anyhow, you might have places that are more "on the road")
* what do you understand under "authentic samurai making"? do you mean pottery? cause that would be unique in kyushu, but "other samurai things" you might find at destinations that are more close to your other spots (e.g. kanazawa, kiso valley,...)

Look at a map of Japan. Plot your chosen destinations on the map. Decide on a sensible route. Use Hyperdia (hyperdia.com/en) or Google Maps to find train routes (Hyperdia allows you to select for JR only).

HyperDia allows you to select for JR only

As to HyperDia's categorization of railway sections as JR,
there is a hidden exception which can appear in search results.

A though train which goes on JR and non-JR sections is considered by HyperDia as a JR train going on a JR-only route, even when the train is actually on a non-JR section.
One example is JR-Izukyu through Limited Express trains, which runs by Kawazu Station.