Has everything have to be planned on a Japan holiday? Is there any place to improvisation?

I have been travelling since my 20s and I've done my fair share of traveling around South America / Africa / Europe / South East Asia. Almost always in trying to spend all my holidays in one month trips, except a whole year of backpacking in my 30s.

The rant: I really like a more relaxed, "freestyle" way of traveling. Normally I sketch a draft of what I want to visit and just book my first days accommodation in the country I'm going to. Then I extend my stay or change plans on the go. Book my stays the day before or even when arriving on a town/city. That almost always worked fine and we could enjoy or holidays without having to plan that much and being able to adapt to weather/preference, or stay more on place that you really enjoyed.

So, this year my SO and I decided on going to Japan, I really like the country and I'm curious, but never researched a lot about traveling there. We book our flights 3 months in advance, which… for us it's kind of early and started the "sketch".

Then I learned about getting tickets always a month in advance, them selling in minutes… At first I thought, well… maybe it's only Ghibli / Sumo tickets. But then the lodging you can find online on small areas runs out fast (i.e: Fuji nearby towns, Nakasendo trail towns, Kumano Kodo…) and I keep seeing people planning for 2025 trips…

I can see how there are so much "I'm feeling overwhelmed" posts. And I'm not enjoying my pre-trip by having to plan that much.

My questions are: should I radically change my way of traveling for this trip? Or is it possible to improvise?

1 About accomodation: What are your recommendations for having a little more flexibility? Will we end only with the more expensive options for lodging?

We are going for a month on 15Sept-15Oct and plan to do Tokyo-Fuji-Nakasendo-Kyoto-Osaka-Nara-Kumano Kodo… and the rest … is still a mistery.

Even if we can kind of improvise a little, any more weak links I might be overlooking? Any tips on not having everything booked?

I'm under the impression that local places are not on booking/agoda. Any tips on finding those? Are those usually avaliable on the spot?

2 About transportation: What about buses / trains / planes? Any routes that could be a problem?

We kind of plan on doing more "non typical routes" if we can. I.E: go from Tokyo to Kyoto by getting a bus to fuji, then a bus to the Magome/Tsumago area, then trying to get a bus to the Takayama area and Shirakawago… and then making our way to Kyoto (still havent' researched what to visit and… if it were any other country I might imprivise on the fly). Would that be very inconvenient?

Sorry if the post is a little bit messy (I knew it was rant-y so I flagged it as that 😉

Edit: Thank you for all your answers! And sorry if this was more a rant than it should be, or if the tone was not the best. I learnt a couple of good tips about being more flexible in Japan, and I hope I can find a compromise between not having everything planned and not missing things!