15 day 14 nights in Japan

Hi there,

My boyfriend and I are planning our trip to Japan for a total of 15 days and 14 nights.

12/11 at 3:15pm Arriving in Tokyo Haneda Airport - planning to stay in Shinjuku area
13/11 - 18/11: exploring Tokyo, Disney Sea, Tokyo Museum, Shibuya etc.
19/11: Travel to Hakone from Tokyo in morning, go to onsen theme park & stay the night
20/11: Travel to Kyoto from Hakone in morning
21/11-22/11: explore Kyoto: Sagano Bamboo forest, Kiyomizudera Temple, etc.
22/11 afternoon, travel to Osaka
22/11-25/11: explore Osaka: Osaka Castle, Momofuku Ando Museum etc.
(Day trip to Nara) 26/11: Leaving at 11am at KIX airport

My questions are:

1) Will it be cheaper to pay for a JR pass for 14 days and just buy point to point ticket on 12/11 or 26/11, OR buy point to point tickets or Kansai pass for the trip?

2) will the JR pass cover all the areas I am travelling to and from? including places I'm exploring in Tokyo, Kyoto and Osaka?

3) if the point to point tickets are cheaper, by how much?

4) any other tips for first time traveller to Japan in regard to public transport?

Thank you