I recommend that you choose the plan that go directly to Yugawara you wrote first. The route through the Shinjuku is a detour, The time required to Yugawara from Narita, JR Tokaido Line is shorter than via Odakyu Line. I made a comparison of the cost for both plans. There was no difference so much as a result. However, if you want to use time effectively, I recommend that you choose a plan first.
Whatever you choose the one, I will let you know the following to you.
a. It is recommended that you use the N'EX Direct Tokyo Ticket to Tokyo area from Narita. There are several means of transportation between them, but I guess that in consideration of the time of transfer, and that use of the Narita Express to buy it is the best.
b. Holder of Hakone free pass is be able to ride in Hakone Tozan Bus to go to Yugawara from Odawara, but the bus is operated only once a day on weekdays. Normally, since difficult to consider that the visitors can use it, it will utilize the train after having paid extra to JR in the section.
Both, the fee for the limited express train other than Narita Express is not included. If you use a limited express train, then the fee depends on separately.
Cost of Plan 1.
N'EX TOKYO Direct Ticket 1,500
OFUNA - YUGAWARA 970
YUGAWARA - ODAWARA 320
HAKONE FREE PASS 2DAY 4,000
ODAWARA -SHINJUKU 1,490(JR) 880(ODAKYU)
TOTAL 8,280 (If Odakyu use: 7,670)
In this case, at the JR EAST Travel Service Center of Narita, when you buy N'EX Ticket, it is recommended that you purchase the ticket to Yugawara from Ofuna. That way, there is no need to settle for additional charges at Yugawara Station.
Cost of Plan 2.
N'EX TOKYO Direct Ticket 1,500
HAKONE FREE PASS 3DAY 5,640
ODAWARA - YUGAWARA 320
YUGAWARA - ODAWARA 320
TOTAL 7,780
N'EX TOKYO Direct Ticket
https://www.jreast.co.jp/e/pass/nex_oneway.htmlHakone Free Pass
http://www.odakyu.jp/english/deels/freepass/hakone/
