PLEASE HELP

Hi!
Would really appreciate some help with planning of itinery and usage of public transport in japan as it can really get very overwhelming. Would require some advice as to whether a JR pass to warranted for my travel. Travel details are as follows

1. Day 1: Arrival at Osaka KTX airport → Shin Osaka station hotel annex
2. Day 2: Shin Osaka station hotel annex → Fushimi Inari Shrine and nishiki market → shimsaibashi
3. Day 3: Shin Osaka station hotel annex → Arashiyama
   *on day 3 we are still undecided if we should take shinkansen or the overnight willer express bus to Tokyo
4. Day 4: Arrival at Tokyo for which we intend to tour shibuya → staying at
   Shinjuku Washington Hotel Main
5. Day 5: Shinjuku Washington Hotel Main → Tokyo Disney sea
6. Day 6: Shibuya-ku → Fuji shibazakura festival
7. Day 7: Shibuya-ku → Tsukiji Fish Market

Sorry for the trouble but I would really appreciate some help with the planning of the transportation. This is in view on Day 4 onwards we will be in Tokyo and I heard from my friends that JR rail is limited for use in Tokyo. I have roughly calculated cost and i think the JR pass is required should we decide to take the shinkansen from osaka to tokyo
THANKS