Check itinerary and seat reservations

Family of 3 travelling to Japan 25th March - 10th April, itinerary as follows:

Arrive Haneda Airport
Day 1-3 stay in Tokyo (possible Fuji day trip)
Day 4 & 5 Tokyo to Kyoto
Day 6 & 7 Kyoto to Naoshima
Day 8 & 9 Naoshima to Hiroshima
Day 10-12 Hiroshima to Kagoshima
Day 13 & 14 Osaka and day trip to Nara
Day 15 & 16 Osaka to Tokyo
Day 17 Tokyo to Haneda airport

My research suggests that a JR pass is marginally more economical and I’m keen on it for the flexibility and convenience. Would you agree or is there another pass/individual tickets that would be better, in your expert opinion?

If we go for the pass, we’re planning to get the 14 pass to be used from day 4. My question is around activation of the pass. If we activate it for day 4 and want to travel the same day, can we make reservations prior to this or only on the day of activation at a JR station? I know we can reserve seats for the other legs in advance but it’s the Tokyo to Kyoto leg I’m concerned about.

Thanks I’m advance, am finding this forum very helpful.