Itinerary questions Narita-Tokyo-Hakone-Kyoto

Hello,

This site looks very helpful and informative. I am hoping to get some help regarding our trip in February. We arrive in Narita on Friday the 10th at 1pm and go to Tokyo for three days then Hakone for one day then Kyoto for three days then back to Narita. We leave back to Hawaii from Narita on Friday night Feb 17 at 7pm. It seems like the one week pass would be the most economical but is that true based on these routes?

Also due to us arriving on Friday afternoon and returning the following Friday night should we take regular transport to Tokyo from Narita and activate our JR pass on our second day (Sat the 11th) so that it doesn't end on our last day in Kyoto and we would still need to go back to Narita for our flight? Thanks for the help.