Confused

Hi, I am traveling to Japan with my son on June 19th, we arrive at Narita and travel to Tokyo, where we stay for 5 nights, then onto Kyoto for 3 nights. We depart from Narita as well. My question is how much will the 7 day all Japan rail pass cover? Does it work for travel around Tokyo and day trips to Mt. Fuji and/or Nikko? I'm assuming it will work to Kyoto, can we travel straight to Narita from Kyoto, or does it go through Tokyo? Would it be better to get a Narita Express ticket as well as a 7 day pass since we are actually there 8 days? I have read some of your responses about seeing Kyoto and Tokyo, thank you for sharing your expertise! I have added several things to do to our list!