1. Remember that you can send your luggage overnight for less than $10. from one city to another or from your hotel to the airport. All you need to carry with you should go in one carry-bag and include what you need overnight and the beginning of the next day.
2. Generally do not make a Shinkansen (bullet) train reservation when you are only a few people. Just go the station and get a ticket for the next train. The trains between Tokyo and Kyoto leave about every 15 minutes. Not having to meet a schedule removes a lot of stress.
3. Buy a phone plan so you can use it here. I bought 100 minutes for an extra $40. from Verizon. But turn your cellular data switch off. You will still get data when you are in a wifi area. Of course if you need data access outside wifi you can always turn it on.
Here is what I did today-- besides packing and arranging shipping from Kyoto and then getting to Tokyo.
Kimono auction all day in Kyoto where I was the only foreigner. I bought very little, learned a lot and loved seeing all my textile pals in one place.