My ideal trip to Japan would have:
nature
culture
food
onsen
shopping (just a little)
Personally 2020/21 being the 20th year anniversary of my first trip to Japan I'd like to spend a couple of days in Takayama, maybe catch an incense ceremony and eat some good food in Kyoto.
HIking Japan - collection of resources
Possible hiking: Kumamo Kodo , Kyoto (KuramaDera and/or another place south of the city, and on the Naoshima Art Island.
Travel to Art Island from Kyoto to Naoshima
Accommodations for Naoshima (stay at least one night, most of one day travel from Kyoto to Naoshima)
Kojima Jeans Street – The Origin of Japanese Denim
JR Passes - Central (to Takayama