I am doing a similar itinerary, but earlier to try and catch the blossoms earlier (arriving week before you).

The one problem I am seeing is Hakone/Kyoto, especially Kyoto. Many top recommendations are already booked up, with exception of maybe top level ($$$$) rooms. For Western hotel in Kyoto, you will have to look into smaller chains or hope for a cancellation. Checking earlier today, Hyatt/Sparriott options are all gone, and Hilton doesn't have a presence (closest is Osaka IIRC).

Good luck on ryokan, top options will be over 1k for 2ppl a night - you are arriving on a weekend during peak season (weekday is cheaper). We are attempting to book Ginyu for 1 night and are waiting to hear back.

IMO, we are fast travelers, but I think you may be too packed in the latter half. We are taking it a little slower than normal to really soak everything in and less hopping, as it is my SO's first time in Japan. We are likely opting to do 3 night Tokyo, 1 night Hakone (maybe two), 3-4 night Kyoto, and back to 3-4 night in Tokyo again. You are potentially losing a lot of time in travel. We strongly considered going to Kobe (also for dinner), but I think we will instead opt to find a restaurant in Tokyo for the experience instead.