We were wusses and organised our whole tour through Inside Japan, who were amazing and so they introduced us to the guides. I am sure you could find something similar via AirBnb or TripAdvisor though.
Our Ryokan was up in the north, because we travelled up there to see the snow monkeys - am not sure if it would be worth the trip that far in October but this is where we stayed. We were upgraded (they apologised a lot, weirdly) to a luxury Japanese style room.
https://yudanakaview.co.jp/en/
Also if you are spending 4 nights in Osaka, do think about Universal Studios, it was epic (and if I remember rightly, the Cup Noodle Museum is out there somewhere too, but we didn't make it). We also visited a very beautiful and interesting museum of traditional buildings (all reconstructed there) in a park in the suburbs which was a real highlight for me. Without Universal, I'd think about 3 nights Kyoto, 3 nights Osaka.
In terms of accommodation, do stay in at least one hotel because the buffet breakfasts are bewilderingly insane. Our top one was the Cross Hotel in Osaka, where I had to have complex negotiations with the offspring around eating salad in exchange for browsing the pudding selection each morning.
Also, eating is quite complicated because of the language barrier. We found it pretty much impossible to go anywhere unless they had an English menu, and self catering - beyond eating onigiri from convenience stores and sushi from department store basements - is quite hard for the same reason. We had a self-catering bit in the middle, for respite, space and doing the washing and I had no idea what was washing powder in the konbini convenience stores, never mind what the food was. And vegetables mostly occurred at breakfast, so we bought a lot of apples.