is it cheaper to buy JRP or individual tickets

mY ITINARY
day1 - arrive Narita airport
day 2- sightseeing in Tokyo
Day 3- Tokyo- hakone stay in Hakone
Day 4- Hakone- Kyoto stay in Kyoto
Day5 - stay in Kyoto
Day6 - Kyoto-Kobe - stay in Kobe
Day7 - Kobe - Osaka - leave from Kansai airport

so not sure if i should buy the 7day pass? when i was trying to work the costs it appeared to be cheaper to buy individual tickets. Plus not sure if the JR pass can be used in Tokyo & Osaka for metros & subways?
Also finding the railway site a bit complicated to use - eg Hakone - kyoto route shows the trains coming back to Tokyo from Odawara & then going to une & Yumuto - which should not be necessary as per my knowledge?