For those that need help planning an itinerary for Japan, I’ve posted here more details on the plan we did, the research on the cost and the logistics on where to stay and how to get there.
The itinerary we did starts and ends in Tokyo during autumn season (Nov-Dec). It’s by no means a comprehensive exploration (since we only had 2 weeks), but I think we did cover the highlights of the places we went to.
Kyoto in particular is a beautiful place to see during autumn because of all the vibrant colors.
If you have more time to spend in Japan, then you can easily add more days in Kyoto/Osaka/Hiroshima and Tokyo. But Shirakawa-go & Takayama are I think just right for 1 day each place.