In 1983 I accompanied my husband and the Australian volleyball team to
Japan with my two girls (ages: 3 yrs and 7months). I soon realised that
travelling with the team was a mistake and ventured off on my own. I had
nothing previously arranged.
A ryokan was recommended in Kyoto that was a fantastic expereince. Unfortunately I can't track down the name, however it convinced me that the ryokan expereince was the only way to go. When I went back to Tokyo I chose a ryokan rather than a hotel and found it was much cheaper and friendlier. Travelling with a baby and a toddler was not easy but the ryokans allowed me to have the true Japanese expereince even though my sightseeing was limited by what one can do while entertaining two children.
We went in November in time to see the fall colours - fantastic. If you contact the Japanese tourist office they should be able to provide you with a list of ryokans that are reasonable and also welcoming to westerners. Ditto the advice to read up on Japanese etiquette. I suspect I was forgiven a great deal because I was travelling with small children.
I am sure you will have a fantastic experience. I envy you!
Regards, Connie in Sydney