7 or 14 day pass

Daniel
We are changing itinerary starting Tokyo arrive late 5/23 stay in Tokyo until 5/26 then to Kyōto from 5/26 to 5/28 then to Kayosan from 5/28 to 5/29. Then on to Naoshima on 5/29 until 5/31 Then back to Nara 5/31 until 6/2 wanted to go to Hakone for 6/2 leaving 6/3 back to Tokyo and leave Henada on 6/4 in AM

We had issue with trip from Nara to Hakone. Is it doable using JR Pass? If so should we get a 14 day and do we need Green Pass. Finally are connection on air lines easy and is it best to have luggage sent ahead. If so who makes arrangements?

Many thanks
JOHN