If you have the budget, I suggest you consider a bike frame with S&S couplers or a Ritchey Breakaway. Either of these will allow a full size road bike to pack in an airline acceptable suitcase. It also allows you to take the bike on trains, buses and taxis without much hassle. I have the Ritchey Breakaway Ti/Carbon bike and it rides just like any high end bike. You can get a good price on this frame and/or the whole bike from
http://www.gvhbikes.com/ (I got mine there and the price and service were great).
Just to give you an idea of how convenient this bike is, I have taken it on business trips and ridden it in Munich, Germany as well as Tokyo and Osaka, Japan. I have also taken it on vacations to Hawaii and Florida. Never has an airline given me any hassle nor have I ever been charged extra for checking the bike as luggage.
As for riding in Japan, others have already suggested stores and websites where you can hook up with local riders. When I rode in Tokyo and Osaka, I just wanted to get out on the streets and ride hard and fast for 60 to 90 minutes before my business meetings started. Thus, I wasn't looking for a group ride. Tokyo and Osaka don't wake up early. If you are out riding by 5:30 AM, you will have even the busiest streets almost completely to yourself which is quite fun. However, by 8 the traffic really picks up. At that time, it feels like riding in most big US cities. In particular, Tokyo felt a lot like riding in New York City (except on the other side of the road ;-). I grew up riding in NYC, so this didn't bother me, but I have heard lots of riders who are used to suburban / bike trail riding complain about their discomfort at riding in an urban environment. I actually had more difficulty in Osaka as I wandered onto a very busy street after 7:30 AM and was not quite sure of my directions. This caused several cars to honk at me (which I believe is much more serious in Japan than in the US). I don't think I was in any real danger, but it did feel a bit uncomfortable. With a bit more experience and better familiarity with directions, I'm sure it would not have been a long term problem.
Good luck and enjoy Japan,
Ira