3 Week Itinerary & Travel Questions

I'm sure you guys get these questions all the time, but after researching myself for a long time, I am kinda overwhelmed by all the options and would like to ask here for some advice. Context: My girlfriend and I are planning a 3-week trip through Japan in September.

The main issue I am having is figuring out if the JR pass (or any other type of pass) is worth it within the 3 weeks. I used some online calculators that give me some estimation, but again there are so many options. I am considering just buying the 21 day JR pass for the convenience, but don't want to spend money unnecessarily. What would you suggest for the below travel plans? If the 'To' column is empty, it just means we are exploring within the 'From' area, probably by walking and/or using the metro.

Day From To
1 Narita Airport Tokyo
1 Asakusa (Tokyo)
2 Meiji Shrine (Tokyo)
2 Harajuku (Tokyo)
2 Shibuya (Tokyo)
3 Asakusa (Tokyo)
3 Kappabashi (Tokyo)
3 Ueno (Tokyo)
3 Ameya Yokocho (Tokyo)
4 Central Tokyo
4 Ahikabara (Tokyo)
5 Tokyo Kawaguchiko
5 Kawaguchiko Tokyo
6 Tokyo Nikko
6 Nikko Tokyo
7 Tokyo Kyoto
7 Fishimi Inari Taisha (Kyoto)
7 Higashiyama & Gion (Kyoto)
7 Pontocho alley (Kyoto)
8 Arashiyama (Kyoto)
8 Kinkaku-ji Temple (Kyoto)
8 Central Kyoto
9 Kyoto Osaka
9 Osaka Kyoto
10 Kyoto Nara
10 Nara Kyoto
11 Kyoto Kobe
11 Kobe Hiroshima
12 Hiroshima Miyajima
12 Miyajima Hiroshima
13 Hiroshima Himeji
13 Himeji Kanazawa
14 Kanazawa
15 Kanazawa
16 Kanazawa Shirakawago
16 Shirakawago Takayama
17 Takayama
18 Takayama Hida-Furukawa
18 Hida-Furukawa Takayama
19 Takayama Kamikochi
19 Kamikochi Takayama
20 Takayama Matsumoto
20 Matsumoto
21 Matsumoto Tokyo
21 Tokyo Narita Airport

Anyone have experience with a similar itinerary?

I hope this isn't too long haha. Thanks in advance for reading and for any suggestions and advice!

TLDR: If/what travel pass to buy? Any advice on 3-week itinerary?

by Tuur013