For my experience to bring my road bike to Japan by air flight, this is the best way to go easy in Japan, to divide 2 boxes (below 200cm).
You can ship or collect them at the luggage counter at the almost of all airports if the luggage size is below 200cm.
The important tips.
In Japan, the space for the large size luggage (over 160cm) in Shinkansen (Bullet train) is not enough capacity and the rule to book it is different between Tokaido Shinkansen(Tokyo- Shinosaka) and other Shinkansen lines.
Other local trains tend to have less space for the oversized luggage.
If you use the train as your mode of transportation, you need to allow extra time to avoid crowded times and to wait for the next train if you can't find a space for it.
When you bring your bike to Japan for your cycling trip, it is important to prepare the delivery the bike case between the airport and hotel in advance.