Kyoto to Tokyo with the JR 7 day pass

I'm getting the JR 7 day pass for the 1st leg of my Japan trip from Haneda Airport to Kyoto to Tokyo. I'm staying in Kyoto for 6 days with separate day tours to Hiroshima/Miyahima, Nara and Arashiyama/Sagayo. On the 7th day, I'm leaving Kyoto headed to my hotel in Tokyo which is a minute walk from the No.2 exit of Ueno Subway station, a 2 minute walk from UENO Japan Rail station and a 6 minute walk from Keisei-Ueno station. Please advise on how to get there with the JR pass.

Here's the 2nd leg of my trip: I'm staying at the Tokyo Hotel for 3 days. My plan is to take a day trip to Kamakura and for the remaining time explore Tokyo. From Tokyo, I'm flying out of Narita. Please advise what's my best option of transportation.

Thank you!