Hi there,
Let's have a look at normal ticket prices and see.
Narita -> Kyoto ¥ 15,530
Kyoto -> Odawara (for Hakone) ¥ 11,550
Odawara --> Tokyo ¥ 3,440
Tokyo --> Narita Airport ¥ 2,740
For a total of ¥ 33,260 the 7 Day JR-Pass is ¥ 28,300 so you would save at least ¥ 4,960 you can also use the pass on local JR Lines in Tokyo to save even more.
The Journey between Narita Airport and Kyoto is about 4 hours. So if you would take the train from 14.30 you would arrive in Kyoto around 18.30. Maybe the trip is a little bit in the long side, however you won't have to change trains between Tokyo and Kyoto so possible you could catch up on some sleep.
When you visit Hakone, Odawara is the best stop when you can from Kyoto. From here you can take a private railway into the Hakone area. A Hakone Free Pass may be of use when you travel around there, as it allows for free travel in the Area and comes with some nice discounts too!
Hope this helps!
-Daniel