Basics
If you ship your bike by air, I recommend you use Tokyo/Narita, Kansai, or Fukuoka airports are probably best. Japan Automobile Federation (JAF) offices are nearby. JAF must validate your carnet (see Entry) before you can go through customs. Be sure to contact JAF before coming to Japan. Get insurance before you pick up your bike.
Picking up your bike
See THIS report from a German who shipped his motorcycle to Narita Airport near Tokyo. Do not plan to pick up the bike the same day you arrive. You need to go to JAF and get insurance first.
After JAF validates your carnet, visit your shipping company office at the airport then customs. After customs stamps your carnet, you can pick it up at the shipping company warehouse.
The shipping company will probably want you to take the motorbike by truck. Tell them you are traveling by motorbike, and ask to uncrate at the warehouse. They may want you to pay to throw away your used crate. Tell them you are a poor traveler, and you can probably leave the crate for free or a few thousand yen.