Regardless of how you come, you need a carnet to get your bike into Japan. Customs should be easy with your carnet. However, you need to have the carnet verified by the Japan Automobile Federation (JAF). The phone number of the Tokyo office is 03-3578-4910 (81-3-578-4910 from outside Japan), and e-mail is kokusai@jaf.or.jp. You need to take the original Carnet to JAF, not a copy. Verification only takes about 10 minutes if you contact JAF in advance. They will have all the paperwork ready. Contact them before you come to Japan; sometimes they don't answer e-mail fast.
Also, ask for a Japanese language copy of the laws on foreign vehicles in Japan, if you don't get it automatically. It is helpful in case you are ever stopped by the police--most don't know you can drive with a foreign license plate. You can print it out here (in Japanese) if you don't get a copy from JAF.
You are required to have insurance in Japan. You can get this at any motorcycle shop. I think the minimum coverage is three months. Unfortunately, a small bike shop in a country town like Fushiki may not be very helpful (no English, never seen a foreign-registered bike)...
If you ship the bike and fly to Japan, stop by JAF in person and get the paperwork done before going to pick up the bike. JAF offices that do this work are in Tokyo, Nagoya, Osaka, and Fukuoka. See the web site http://www.jaf.or.jp/e/list.htm for directions.
If you come from Vladivostok, the Toyama JAF office will do the paperwork for you if you contact Tokyo beforehand and fax your carnet to them.
Entering at Wakkanai from Sakhalin will require that you send the Carnet (not needed in Russia) to Tokyo for verification and then sent back to you. However, someone will have to appear in your behalf at JAF in person to do the paperwork.
Unfortunately for German, French, and Swiss riders, you are not allowed to ride your bike without registering it. Nobody I know has got in trouble for it, as far as I know though. JAF will not give you a copy of the laws on foreign vehicles in Japan. Supposedly, international drivers licenses for those countries are also invalid in Japan. Something about not signing the same international treaty...
All information is subject to change. Please let me know if you find situations have changed.