Help! :)

Hi!
Wondering if someone can help/give us some advice.
Were due to visit Japan late June/early July but were struggling with working out our routes!

We arrive in Tokyo on 21/06/2020.
We leave Tokyo/Shunjuku on 24/06/2020 for an overnight trip staying at Hoshinoya, Fujikawaguchiko.

25/06/2020 - Down to Osaka for 4 days including a day trip to Kobe & Nara

29/06/2020 - Over to Kyoto

Then back to Tokyo on 02/07/2020

I keep reading different things some are saying all the journeys would be covered under JR some say parts are covered. I know we need to get them just working out whether we need a 14 day pass ( quite possibly ) and if there is any further costs if some aren't covered by the passes.

Please can you help/advise us? - I'm so lost!! :)

thank you