I highly recommend the Tsukiji fish market in Tokyo, it opens very early but we got there around 7:30 (late) and enjoyed walking around without the huge crowds. There are a few small restaurants there as well, some of the best sushi we have had even though it was for breakfast. There is a park nearby that is very nice as well.
You can do a walking tour of many of the shrines in Kyoto, and we took the bus to the "big" tourist attractions without much of a problem. A Japan or Kyoto-specific guide book is a great idea. Have fun!