I'll add a few more comments.
1. The rental cars in Japan are all (or almost all) automatic transmission.
2. The built in GPS can be tricky to use, be sure to get a map from the rental car company because it may have the numeric codes for various destinations. It's easier to type in the numeric codes than it is to type in the names/addresses of places. Alternatively, just get a data SIM card and use Google maps on your own phone to direct you.