In April 2017, we used 7-day standard Japan Rail Pass to do a rail and cycling tour of Japan. We did a day trip on the Day 1 to Kagoshima then 5-day trip covering Shimanami Kaido, Mt Fuji and Noto Peninsula, with the last day travelling to Osaka to catch our flight from Kansai Airport. This is our brief itinerary for 7 days with further posting for each route to follow.
In Japan, traveling on the train with a bicycle is permitted, even on Shinkansen with no extra charge. You can take a bike on any train at any time for free of charge if you store it in a bike bag called ‘Rinko bag’ 輪行バッグ.