Here are some tips on how I did it, and how you can too.
Step 1: Plan Your Trip
Hokkaido in September was a good choice, in spite of the fact that it rains (a lot). Campsites are plentiful and cheap, and there are loads of natural hot springs, mountains and good roads. August would have been crowded, and October would have been cold. I rented out my apartment, which gave me a $1000 credit toward my plane ticket. That was $1230 RT from San Francisco, CA to Asahikawa, Hokkaido.
Asahikawa is well situated. My plane was late, but I still had time to assemble my bike and gear, and ride the 14 km to a free urban campsite, where I bought fuel and food for my trip.
I brought my own bike-
ANA still flies your bike for free, and will guarantee that policy on connecting flights- even if you have to spend a night in Tokyo and switch airports. They are nice, the food is good and they even allowed me to return with overweight bags. Twice - no charge.
I packed light-
I put my bike in a Japanese bike bag for the flight, and used compression sacks to get it all in there, tent, bags stove- the works. I can carry it by myself, even with the bike packed up. This means I can take a bus or train should I break down on the road. You might use a bike box, or consider buying a "rinkyou bukuro" bag for your return trip. That way, you can ride back to the airport and pack your bags.
I flew to my start and endpoints-
JapanRail passes are a great deal, but it's very hard to pack and carry your full sized bike and get it on and off trains. Perhaps you should save it for another trip or a trip- or use it with your folding bike.
You might take a Japanese Class-
Or go to a local Japanese restaurant with a phrase book or dictionary and chat up the staff. It was easy for me to find and trade language skills in San Francisco, but I got so much out of a conversational language class that I really have to encourage you to do it. People will really want to talk to you if you show some interest in learning Japanese.
Get hold of a Touring Mapple-
The Lonely Planet guide is fine, sure, but you want to travel Japanese style and meet Japanese people, right? You might want to cut out some pages, and leave it at home. The Touring Mapple is an amazing tool- if a bit mystifying at first. Find your next campsite, hot bath and ATM. Convenience stores have 1000yen maps by Mapple, and are adequate in a pinch. Your new Japanese friend can help you order one on line, and tell you what the symbols mean, or you can take your chances and try to buy one when you get there. Many large department stores have book shops (as well as supermarkets!) There is also a magazine called 0Yen Mapple, and if you can get it for your region, you should.