How far apart are some of the tourist spots?

I am doing the 12 day suggested itinerary http://www.japan-guide.com/e/e2400_tokyo_10.html and I click on the city name to see what they have to offer. Obviously I won't be able to see everything especially with big cities like Tokyo and Kyoto.

What about the smaller cities? I know shrines and temples aren't right next to each other or anything but I'm trying to calculate travel time with the day that I'll be in those smaller places. Will the bus rides and what not take me more than an hour to go to different things?

You shouldn't have to spend more than about 30 minutes travelling between sites in the cities on that itinerary, as they are generally compact places. In most cases you'll spend even less time getting between the major sites.