Another travel thread: Any tips for Japan (Tokyo, Kyoto especially)?

OK- Have our lodging set. Will be in Okinawa for several days, then flying to Osaka and taking the train to Kyoto. Will be there, staying in a ryokan for 2 nights (1 1/2 days or so) and then taking the train for 1 day in Tokyo (staying in the Shinjuku district) for one night before heading back on the train to Narita. We have our Japan rail passes and the hotels set (used hotel points for some of the stays, got adventurous for others). Any “must see” stuff in Kyoto (have the bamboo garden and golden palace on the list) and good walking tour sites in the Shinjuku section of Tokyo?