Valid for subway or bus inside cities ?

Hello, I'm travelling to Japan for 2 weeks from 19 April (early arrival) to 1 May (early depart)
Does the JRPass includes subway or buses in Tokyo, Kyoto or other cities ?

And does it compensate to acquire the 2 weeks pass for the following or similar itenerary:
19 - Haneda-Tokyo
20 Day trip to Nikko
21 Tokyo
22 Day trip to Fuji area
23 Tokyo-Matsumoto
24 Matsumoto-Takayama (by bus. Does it exist JR bus lines to do it ?)
25 Takayama-Kanazawa
26 Kanazawa
27 Kanazawa-Himeji-Kyoto
28 Kyoto
29 Day trip to Nara
30 Kyoto-Tokyo
1 Tokyo-Haneda

Thanks for you tips