First Time To Japan - Kyoto/Tokyo Advice
We used a tour guide for a day in Kyoto, and were very pleased. This allowed us to see more than we could have done on our own, and added immeasurably to the richness of our experience. Kyoto needs a few days, but barring that be aware that Public transportation is good but not always as convenient or as easily accessed. Taxis are all over, reasonably priced, and useful.
We used Naiki Doi and highly recommend him.
http://www3.ocn.ne.jp/~doitaxi/