[Early flight from Narita airport. Hotel shuttle bus?]

Our flight from Narita departs at 9 a.m. For peace of mind, I believe it would be prudent to return the rental car a day prior and spend our final night at a hotel near the airport. It appears that these hotels are not situated within the airport terminal, unlike those at Kansai or Nagoya. Do hotels near Narita have shuttle buses to the airport early in the morning?

[Japan Rail Pass use on Yamanote Line and subway]

I got Japan Rail Pass for 7 days. I'm going to use it to travel from Tokyo to Kyoto and Osaka. Where can use the JR Pass while staying in Tokyo? Can it be used to travel on Yamanote line and subway?