1) Friendly Airport Limousine (orange and cream colored)buses run to most hotels in Tokyo. It will cost you ¥3000 per person (no discount for round trips). It should take about 75-90 minutes....
3) There is no Shinkansen link from Hakone to Kyoto. You will have to return to Tokyo or go to Shin-Yokohama or elsewhere for the bullet train. Type in the stations on this website and it will give you itineraries:
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3) Kyoto to NRT may be about 4 hrs depending if you catch a good connection at Tokyo station....