tokyo kyoto osaka hankone tokyo

hi

we are travelling in march end to japan for13 days itenary as follows
day1 -- narata to Kyoto
day2 -- Kyoto
day3-- Kyoto
day4--Kyoto
day 5 Osaka
day6--Osaka
day7--Osaka
day8 --hankone
day9 --Tokyo
day10 tokyo
day11 Tokyo
day 12 Tokyo
day13 Tokyo
will the jrpass cover all the intercity travel, local travel within Kyoto Osaka hakone Tokyo (underground bus etc).
how much extra will we have to pay extra we need to pay .
please advice how do we do about should we take a 14 day pass or a 7 day pass and there after normal
regards
parul