I echo the other posters -- the shinkansen is the best way to go. If this is your first time in Japan, I'd recommend taking that leg even if you didn't have to fly into Narita and/or didn't have to visit someone in Kyoto. This is one of the world's truly great train journeys, the food and service are top notch, and if you get lucky, there's a once-in-a-lifetime view of Mt. Fuji.
It's true that Japan, esp. Tokyo, can be discombobulating, that you'll be tired, and that the culture and language are very different. But honestly, even before I spoke the language at all, I felt more comfortable in Japan than I did in France. If you need help, and you can say the name of your destination, people will go far out of their way to help you even if they don't speak English. Even in Tokyo Station at the height of rush hour, people will come running to help a foreigner in distress (I tested this firsthand on my last trip, when I tripped and fell on my face, suitcases flying, and I was surrounded by people trying to help me up and asking if I was OK before I even realized what had happened).