I’ve done 2 bike trips to Japan in October
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October is still warm but the temps on northern Honshu are just starting to become more tolerable. It will still be humid. So it can be a great time. However it is also the heart of Typhoon season and both times we got to experience them. The second trip they where more than we bargained for with over an meter of rain in 24 hours fully flooding and shutting everything down around Nagano.
My advice is to black cat your luggage ahead to each location. It’s very reliable and usually overnight. Best of all it’s cheap.
At the end of the trip you can ship the bikes and all of your luggage straight to your airport terminal and can enjoy Tokyo luggage free for a few days.