We used Japanese guest houses to book our two nights at the Nagase Ryokan in Takayama and one night at Shojo-shin monastary at Koyasan. (Family of four: 2 parents and two teenage sons.)

First, I cannot say enough about Japanese Guest Houses' service for booking...easy, clear and FREE. They were great! (You already have their llink, I see.)

Second, our ryokan stay was a definite high point of the trip. It would have not been the same (not so relaxing) one night. If you can afford it, and you are staying at a high quality one---I recommend two nights.