Over 6 weeks in Japan using public transport

Hi, I am so overwhelmed with the different rail systems and pass options and am hoping some of you can offer suggestions please.

1. We will be in Tokyo for 13 days, so will probably not need a JR rail pass for this part of the trip. What is the best way to pay for rail travel around Tokyo?

2. Which segment of our trip would the JR rail pass be most useful, bearing in mind that we can only get a maximum 21-day pass (with 2 x 7-day passes being an alternative option)?

21/3 Tokyo - Hakone
23/3 Hakone - Takayama
27/3 Takayama - Kanazawa
29/3 Kanazawa - Kyoto
12/4 Kyoto - Hiroshima
13/4 Miyajima day trip
14/4 Hiroshima - Osaka
19/4 Osaka - Kansai airport

Thank you in advance for any advice or tips for our travel.