I only really know Hokkaido as I visit my in-laws there every year. First two weeks of April is probably a bit too cold for most of the routes I’ve done there though.
Others will be more qualified than me to talk about the climate and roads on Honshū, Shikoku or Kyūshū but in general I’ve found it very easy to plan routes and find my way around with very limited knowledge. Get yourself sorted with a data SIM card or portable Wi-fi hotspot and it’ll be easy to navigate.
Enjoy the cities and the cleanliness and find some nice routes that take you across the mountain passes. I’d be tempted to look at a route that will take you from Kyoto to Tokyo and going through places like Osaka, Nara, Nagoya, Shizuoka and Yokohama. Loss of touristy stuff to do in those places and it’s a popular Route that will take you past Fuji. South coast shouldn’t be too chilly around that time of the year. I think.
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