Tokyo to Kyoto & Mt.Fuji

Hello I am arriving at 1:25PM at the Narita Airport and i need to catch the train to Kyoto. We will stay in Kyoto for 3 days and then go back to Tokyo. At some point from Tokyo I want to do a day trip to Mt.Fuji area. I want to buy the pass but I wanted to make sure that 1 I can get to all the places I need and that 2 it is the fastest way. I looked on the Hyperdia site and it says I can get the train around 4PM from NARITA AIRPORT TERMINAL to SHINAGAWA and then get to Kyoto by 7:50pm. But there was a warning that some trips may not be possible on the Rail Pass. Are these options available? Also, because I am traveling Christmas day how can i ensure that we have a seat? I wanted to do the VIP pass.