[jasonbvr]

So after a 12 hour flight you're going to take the train to Tokyo or Shinjuku station (about 1 or 2 hours), then after finding the shinkansen platform and getting tickets (30 mins if you're lucky), waiting for the next train (30 mins to an hour), you will get on a train for another 3 hours of traveling?

That is like 20 hours of traveling. Why are you not flying directly to Kyoto and leaving from Tokyo? I forgot to add the time you will spend going through immigration and getting luggage off the plane (2-3 hours). If you can get a flight directly to Kyoto or one that flies through Tokyo to Kyoto, you would be a lot better off.