I will post actual costs and links after our trip in March.
Total cost for everything (includes food, transport, accommodation, admissions) is $110/person per day for three people by my calculation so far as our air tickets were purchased with points.
Others have done it for less:
http://rtw-travel-guide.com/how-much-does-it-cost-to-travel-in-japan-2013/ The first class JR rail pass for seven of these days is $367 each. We went with first class after some consideration. Given the amount of travel on the train we'll do it made sense for us to have preferred seating for the busier routes.
Accommodation averaged about $75/night for three using Airbnb. A private apartment in Tokyo was only $65 dollars each night! It is small but new, sleeps 3 which is difficult to find for a hotel in Tokyo (usually 2 is the limit so we'd have needed two rooms), and is on a subway line.
Our itinerary is:
Day 1 Tokyo Arrive evening (Airbnb apartment)
Day 2 Tokyo Pokecentre, evening in Roppongi (Airbnb apartment)
Day 3 Tokyo Morning Ghibli Museum, afternoon Akasakusa, evening onsen (Airbnb apartment)
Day 4 Tokyo - Izumo train - rent car (Airbnb apartment)
Day 5 Izumo tour countryside (Airbnb apartment)
Day 6 Hiroshima arrive Hiroshima 1:30 pm ferry to Miyajima return Okonomiyaki evening (Peace Park accommodation)
Day 7 Kobe morning tour of Peace Park with guide afternoon train to Kobe (Airbnb with family)
Day 8 Kyoto train Kobe to Kyoto afternoon and evening tour in Kyoto (Airbnb Samurai bar apartment)
Day 9 Shizuoka morning in Kyoto - leave Kyoto approx. 1pm. - Dinner with family in Shizuoka - get picked up (Airbnb with family)
Day 10 Tokyo morning bus tour of Mt. Fuji lunch with family in Shizuoka leave for Tokyo 3pm (Airbnb apartment)
Day 11 Tokyo open for shopping/requests/last minute ideas (Airbnb apartment)
Day 12 Depart day in Tokyo - fish market tour and sushi lesson (overnight flight)
Day 13 Day in San Francisco (evening flight home)