Transport advice

Will be travelling to Japan on Oct 17

Need help with planning the transport means.

9th Haneda to Osaka

Rough itinerary as follows:
9-14 Osaka:
Planning for Kyoto, Nara, USJ

14-15 Hakone/Fuji
14th noon to check in hotel at Hakone . Hopefully near hakone yumoto (PLEASE ADVICE) Explore Hakone, 1 night stay in Hakone.
15th head to kawaguchiko and explore, end the day at Gotemba then back to collect luggage at Hakone Hotel (please advice if that's a good decision). Head to Shinjuku/Tokyo hotel for the night.

15-20
15th night sleep in in Tokyo.
16th onwards be around Tokyo, might be going Disney.

Need help with the transport route and also travel passes available.

Planning to get 7 day JR pass from 9th-15th. Not sure how to go about with the Fuji Hakone Free Pass, where to buy and also whether it's suitable for the trip.

2 adults!