|I've wanted to go cycle touring in Japan for years, as I keep hearing how good the riding is. This year I got my chance, as I was in Tokyo for a conference (3DV). It was the middle of winter so I headed further South to Shikoku island, which should have been warmer and dryer, except there was unusually heavy snow and rain while I was there. It was still a good ride, 1020km in 8 days mostly on quiet mountain roads.
Route: on Google maps here. The mountain roads are awesome to ride, except the busy East-West routes (197 and 438). The North-South routes cross mountain passes. The more major roads around the coast and through cities have awesome bike paths. The Shimanami Kaido bridges linking a chain of islands between Honshu (the mainland) and Shikoku has an awesome bike trail running alongside it.
Accomodation. There's lots of places to stay, especially on the pilgrim Henro trail (and listed in the Henro trail guidebook), but usually you need to book in advance, in Japanese. There are a few hostels (which expect you to book if you want food). Otherwise the bigger towns have business hotels, and the smaller places appear to have nothing. The food is good, especially if you like oily fish, but it was often hard to find anything open in December (off-season). 8 day trip cost about Y110000 including trains. A phrasebook or guidebook with Kanji would have been useful...
Trains. I used a Ground Effect Tardis bike bag. The best place on the trains/Shinkansen for it was slotted behind the last row of seats.
Maps. I used OpenStreetMap and the tablet app (with offline maps). It worked really well, but without any topographic information I never knew how big the passes were going to be. I had Backcountry navigator with topo maps, but the app was too unstable to use.