14D14N itinerary

Hello travel experts,

My wife and I are traveling to Japan in the first 2 weeks of November. After some googling, I have come up with the below Itinerary. Please take a moment to look through them and answer a few questions i have at the bottom.

1 - Sat Nov 2nd (1/5 tokyo overnight)
-Arrive 3PM and checkin at hotel
-visit Shibuya, Kabukicho, Golden Gai and Omoide Yokocho at night

2 - Sunday Nov 3rd (2/5 tokyo overnight)
-Western Tokyo Full Day (japan-guide.com/e/e3051_west_tokyo_full.html)

3 - Monday Nov 4th (3/5 tokyo overnight)
-Ueno Park
-Asakusa and Odaiba Full Day (japan-guide.com/e/e3051_odaiba_asakusa_full.html)

4 - Tuesday Nov 5th (4/5 tokyo overnight)
-Day trip to Nikko

5 - Wednesday Nov 6th (5/5 tokyo overnight)
-Day trip to Kamakura (morning and noon) and Yokohama (afternoon and night)
-Back to Tokyo

6 - Thursday Nov 7th (1/2 Hiroshima overnight)
-Imperial Palace and Ginza Half Day (japan-guide.com/e/e3051_imperial_ginza_half.html)
-Evening travel to Hiroshima (overnight in Hiroshima)

7 - Friday Nov 8th (2/2 Hiroshima overnight)
-Explore Hiroshima
-Visit Miyajima in the afternoon and evenining (Overnight in Hiroshima)

8 - Saturday Nov 9th (1/1 Osaka overnight)
-Travel to Osaka (overnight in Osaka)

9 - Sunday Nov 10th (1/1) Mt Koya overnight)
-Travel to Mt Koya (overnight in Mt Koya)

10 - Monday Nov 11th (1/3 Kyoto onvernight)
-Travel to Kyoto (overnight in Kyoto)
-Northern Kyoto (japan-guide.com/e/e3950_northern_kyoto_half.html)

11 - Tuesday Nov 12nd (2/3 Kyoto onvernight)
-Arashiyama Full Day (japan-guide.com/e/e3950_arashiyama_full.html)

12 - Wednesday Nov 13rd (3/3 Kyoto overnight)
-Eastern Kyoto Full Day (japan-guide.com/e/e3950_eastern_kyoto_full.html)

13 - Thursday Nov 14th (1/2 Hakone overnight)
-Day trip to Nara then head straight to Hakone (overnight in Hakone)

14 - Friday Nov 15th (2/2 Hakone overnight)
-Explore Hakone (overnight in Hakone)

15 - Saturday Nov 16th
-Morning travel to Narita for 5pm departure

Does this trip make sense? Does it save travel time as much as possible?
14 Days JR pass alone will be enough for travel to all these cities?
When should i activate JR pass?
Is JR Pass used for long distant travel between cities only or is it also used to travel within cities ? Meanning, can i also use the JR pass to travel to various tourist attractions and different parts of Tokyo, Osaka and Kyoto?
Do i need to get different passes for the remaining cities?
What about Hakone Free Pass?

I have yet look into places to stay...but if you have a location in mind, please advise. We are looking for a places where it is easy to travel to all the attractions within the cities.

Looks good to me (though I would not describe myself as a travel expert!)

You can get to all those cities with the JR pass, except Hakone, so that will involve a little extra expense (see http://www.japan-guide.com/e/e5206.html). It's still worth getting the JR pass. You should activate it as soon as you arrive so that you can get from Narita Airport to Tokyo.

You can use the JR pass on JR trains within Tokyo, Osaka and Kyoto. In Tokyo, the JR Yamanote Line connects most of the districts you will probably want to visit. Osaka is fairly well covered as well. Kyoto is not; you will need to use other transport as well to visit the tourist attractions, unless you are prepared to do a lot of walking.