16 nights itinerary

Hi,

My family (boy 3.5 years old) and I are planning to visit Japan for the first time in a few days, any chance you can validate our itinerary?

Day 1: arriving in Japan (Tokyo Haneda Airport)
Day 2: Tokyo
Day 3: Tokyo
Day 4: Tokyo
Day 5: Kawaguchiko
Day 6: Kyoto
Day 7: Kyoto
Day 8: Kyoto
Day 9: Nara
Day 10: Osaka
Day 11: Osaka
Day 12: Osaka
Day 13: Kobe
Day 14: Kobe
Day 15: Hiroshima
Day 16: Tokyo
Day 17: leaving Japan (Tokyo Narita Airport)

We have purchased the JP Pass and are planning to activate it on Day 5. Having said that, due to peak season, I believe we should book the seats in advance, right? (for buses/trains, etc.). Is there a general website where we can do that or there are different websites?

Also, what's the best option to travel from Tokyo Haneda Airport to Akasaka Minato? Arriving on March 31 @ 22:45 so might be tricky considering it's weekend.

If you can provide some feedback, suggestions, etc. that would be much appreciated.

Regards,
Eduard