Itinerary and japan rail advice

Hi,
we are travelling to Japan arriving in Osako on June 28th and departing from Tokyo on July 15th.
Our itinerary is as follows
June 28 - july 2nd Kyoto with day trip to Nara,
July 2nd overnight in Kurashiki
July 3rd and 4th Mijajima
July 5th and 6th Tsumago
July 7th and 8th Takajama
July 9th and 10th Kanazawa
July 11th - 15th Tokyowith trip to Nikko leaving on night of 15th.
We are pretty happy with balance of trip between cities and quieter locations so gererally my questions are does this route make sense as to day to day travel or can it be refined or adjusted. Secondly what travel passes should we use I have read about Haruka and Icoca pass for travel to Kyoto and around but it is after this that I am getting confused. Would the 7 day pass good value to use from July 2 to July 8, take the bus to Kanazawa stopping in Shirakawa go.
Visit the gardens on 10th and then just pay for singles on train to Tokyo on the 11th. Any advise or help would be much appreciated.

Only comment:

Two nights on Miyajima seems way too much. We did a day trip and climbed the mountain and saw it all on a cold winter day.