This website will give you an idea of tolls and routes.http://global.c-nexco.co.jp/
Use Google Maps to determine approximate drive times. Click on get directions, enter Tokyo, Japan and Kyoto, Japan, then click "by car". It's approximately a 6 hour trip on a good day.
I, like you, enjoy driving at times and having the freedom to get off the expressways and seeing the countryside.
Have fun!!