JR pass 7 days for 12 days holiday

Hi,

I am travelling for 12 days with the following itinerary:
Day 1 : arrive to Osaka at 6.10 pm
Day 2 : Osaka
Day 3: osaka - kyoto (in the morning)
Day 4: Kyoto
Day 5: kyoto (will go to arashiyama and surrounding)
Day 6: Kyoto - Tokyo
Day 7 : Tokyo
Day 8: Tokyo
Day 9: Tokyo
Day 10 : Tokyo
Day 11 : tokyo
Day 12 : tokyo - to narita airport

The significant fees is travelling from Osaka-kyoto( approx 2110-3400 yen), kyoto- tokyo( approx 13200 yen), as well as tokyo - narita (approx 3000 yen) and each I make it one way rather than two ways journey for each town I visit.
Firstly I am planning to buy 7 days JR Pass, however after I recalculating the fare fees using hyperdia, it seems it is not ecomonical rather than buying individual tickets. Please correct me if I am wrong.

secondly, I was informed that there is a one day pass ticket in osaka. If I am planning to go to osaka castle, osaka park as well as shopping area in namba/kita/dontonburi (my hotel location is namba) , does it more cheaper for me to buy indifvidual tickes rather than one day pass

thirdly, if i am not using JR pass to travel with, is there any preference bullet train/shinkansen/train/metro/subway that I should choose eg cheaper or more time table ?

Grateful for your advice