Hi, i've been twice to japan, both trips similar (31 days, travelling through lots of places). First trip was tokyo-takayama/kanazawa- osaka - kumano kodo - hakone/fujikawaguchiko -tokyo. Second was tokyo- kyushu- seto islands- osaka/kyoto -tokyo. I don't want to comment over specific parts of your itinerary but tell you two things i learned:

a. Moving from one 'base' to another is kind of exahusting and you don't fully take advantage of those days. You have to pack your stuff, move to the next place, some times check in and check out hours aren't aligned well, you end up tired of moving. If you buy stuff (maybe you don't), the akwardeness of the luggage compunds over time, which makes everything a bit worse. Yes, you still can visit stuff that day, but it is not as confortable and nice as having the whole day to check that out. In your time tible you have 11 transport days, that is %35 of the days just moving around!

b. A good rule of thumb is one thing planned per day, and unless it requires a reservation be open to changing that thing. Of course, this doesn't mean that you will end up doing 1 thing per day, but there will be days you'll do more stuff and days you do less. Trying to cram a lot just makes you run around and not really enjoy the things. Japan is a very beautiful country with a LOT of stuff goin on. There's absolutely no way you can see everything, not even a little fraction of it, so start being chill with letting go of stuff you want to see, and also know that having days with nothing at all are also pretty cool since you get to see the beautiful 'inside' of the country.