How to best use a 7 day pass

A group of 8 of us arrive in Tokyo on Sunday, Nov 18. We will travel to Tokyo, Kyoto, Hiroshima, Osaka and back to Tokyo to catch our return flight home from Narita Monday Nov 26. As you can see we are in Japan just over the 7 day limit and don't want to spend more money for the 14 day pass. What is the best recommendation? We will go to Tokyo Sunday and Monday and leave for Kyoto Tuesday. Should we activate our pass on Tuesday and use it for the last 7 days? If so, How much will it cost us to get to our hotel in Shinjuku on hte first day and where do we activate the pass in Shinjuku? I know where to activate it in Narita airport but not within Tokyo.