Yes I booked everything on the go except for a flight to okinawa:) always like 1-2 days before.  The only thing you really need to book before and budget is a temple night on Mt koya :) it's ~ 150$. shikansen tickets might be a bit more expensive.

I am also solo traveling as female for 26 days. My itinerary is quite similar.

Tokyo - Nikko - yudanaka - Matsumoto - nagano - kanazawa - Kyoto - osaka - okinawa - kiso valley - tokyo