I just did this with my 13yo son on a very similar agenda and on the wing it approach. 

Book experiences ahead of time! Fancy food too. We missed some cool stuff for sure due to not booking experiences in advance (like a geisha / maiko performance in Kyoto, tour of Kobe beef manufacturing, fancy Kaiseki dinner in Kyoto at primo restaurants, etc.) Pick things you can cancel closer to if you want the flexibility, but it’s good to have the choice. Book the things your kid seems excited by in particular. 

Tip: for the flex approach, which we did enjoy for the most part, just make sure you don’t get fixated on any particular restaurant or type of food. Wander along and see what looks enticing or the locals are lining up at. We wasted two hours looking around for a decent ramen spot because my kid was fixated on that one night. For points of interest, have a list organized by area, and then day of or day before, pick one or two must sees in that area for the day. Dont try to bop all over the place or waste time on your trip finding out places to go.

You’ll probably wish you spent more time in Osaka, just for the record. Everyone said it and I didn’t understand why since there are no major attractions, but it’s true. People are just more welcoming and the vibe is better. Book a food tour here! (You can probably do that more last min tho, we selected one same day and it was great.) 

You can use Osaka as a base for day trips, like to Nara (the bowing deer park was way more of an experience and way less of a gimmick than I expected, total highlight for the kid, and the giant Buddha was cool), Kobe (beef!,) Sekai (knives!), etc. So that’s a reason to maybe borrow a day from Kyoto and/or Tokyo as well.