Ask advise for my itinerary

I and my husband planned to visit Japan from 31/10/2015 to 13/12/2015. We already visited Japan in February to April of 2008 and visited most of the famous sites in Tokyo, Nara, Osaka, Kyoto, Hamura, Nikko, Yamagata... This year we want to see Japan in Autumn, but we want to plan a best itinerary at low cost, we would like to have your good advice which save accommodation (hotel, shared room) and use JRPass the best.

Your advice ASAP would be appreciated.

P.S. We can stay free at my daughter room in Tokyo Setagaya-ku in 7 - 14 days only (even on the arrival date or before leaving Japan).

Best regards,
Phuc Nguyen