What is suggested for my train travel

Unfortunately, if you are not making a round trip, a JR Pass would not be cost effective. You can ride the bullet train with regular tickets though.

Depending on your plans, one of the Kansai regional passes might save you some money:

http://www.japan-guide.com/e/e2357_kansai.html

Kyoto and Nara are the most interesting cities to see though, and if you can see Himeji Castle, which is Japan's finest, it will be well worth it.

Your kids probably would love the walk though in Fushimi Inari Shrine in Kyoto - it is something they'll never forget:

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

And the cherry blossom mecca of Japan is in Nara:

http://www.japan-guide.com/e/e4150.html

I am sure you are already aware that you will be in Japan in cherry blossom season - it will be a lot more crowded in many places. But there are also many good places to see the blossoms:

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

For the Tokyo area, you can extend your Japan experience by also taking a few days trips to popular places like Nikko, Kamakura/Enoshima, and Hakone.

There are some day passes that can help you there too:

http://www.japan-guide.com/e/e2357.html