Tokyo-Hakone-Kyoto-Nara-Tokyo

A 7-day trip plan. What is the best means (budget & time) of transportation. I am confused with the JR, Rail and shinkensan lines. Thx.

A 7-day trip plan. What is the best means (budget & time) of transportation. I am confused with the JR, Rail and shinkensan lines.

The 7-day JR pass is 28,300 yen.
http://www.japanrailpass.net/eng/en003.html

Day 1) Tokyo to Odawara, then Hakone
Tokyo 7:56--(Shinkansen Kodama)--8:37 Odawara
From Odawara, the JR pass is inapplicable. You might buy the 2-day Hakone Free Pass originating at Odawara for 3,900 yen.
http://www.hakonenavi.jp/english/freepass/index.html
Hakone Loop guide ( It takes about 4 hours minimum.):
http://www.odakyu.jp/english/freepass/hakone_01.html

You could have your luggage sent to your hotel by the evening by leaving it at the courier in Hakone-Yumoto Station for 500 or 600 yen.

Day 2) Odawara 10:09--(Shinkansen Hikari)--12:14 Kyoto

Day 3, 4) Kyoto
Day 4) Day trip to Nara by JR
Day 5) Return to Tokyo
Day 6) Getting around Tokyo
Day 7) Return to Narita Airport

This is just a model itinerary. You could arrange it as you like. Making a day trip to Himeji or Hiroshima is viable from Kyoto by Shinkansen.

Train schedule search:
http://www.hyperdia.com/cgi-english/hyperWeb.cgi