We have a wonderful 8 days in Japan prior to our cruise out of Yokohama that also stopped at 5 Japanese ports.
We love Japan and its people. Japan is one of the cleanest places in the World and its people are among the most helpful and polite. The food is excellent and Japan is not as expensive as most people think.
Here is my detailed review of our travels in Japan as well as our cruise. It may help you with hotels and tours among other things.
http://www.cruisecritic.com/memberreviews/memberreview.cfm?EntryID=518503&et_cid=2531924&et_rid=17221689&et_referrer=Boards
Kyoto is fantastic. I suggest staying there at least two days. We took a tour of Kyoto and Nara for three days from Tokyo and it was great. I found the tour on Viator.
You can visit the many temples, palaces and shines on your own, but it is not easy. Taxis are not cheap and the key sights are spread out. I suggest joining a tour. Don't miss the Golden Pavilion. It is amazing.