Basics
If you ship your bike by sea, I recommend you use Tokyo, Yokohama, Nagoya, Kobe, Osaka, or Fukuoka port. These cities have international airports and Japan Automobile Federation (JAF) offices 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
Contact your shipping company and get directions to the warehouse. Japanese ports are VERY BIG, so ask for directions in advance.
After JAF validates your carnet, take it and your bill of lading to the customs office. After customs stamps your carnet, you can pick it up at the shipping company warehouse. Customs usually takes about 30 minutes.
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.