How do we organise an airport / train transfer at the end of our stay in a house?

A transfer to the airport (Tokyo Haneda or Narita, and Kyoto Kansai Airport) can be made in a shared shuttle or by train.

The shared shuttle has a tendency to pick you up early, allowing a large safety margin due to possible traffic jams that can cause delays. However it has the advantage of picking you up right outside the house. Note that it must be booked at least 3 days in advance.

With the train there are no traffic jams so it's more dependable. But it is a bit more expensive (you will have to get a taxi or bus from the house to the nearest train station first) and it requires a little more physical effort to reach the train once in the station.