Is there a website or printed reference to figure out how much certain stretches of toll highways will cost?

Perhaps this link will help you, I use it to plan my travel through Japan. You have to enter the starting and arrival addresses, all in Japanese. The site will then find the best way to go there with 2 options, either using only free roads or including toll ones (like highway).

Navitime, plan your travel (in Japanese)

For example : try to go from Tokyo to Shizuoka (I just choose random addresses in both cities, no idea what it corresponds to)

tokyo : 東京都品川区大崎２丁目４-５
shizuoka : 静岡県静岡市葵区赤松５-２４

Using highway it would cost you: 4500 yen, taking 171.km, 2h50
without toll roads: 174.7km, 6h20

Hope this will help you

Thanks so much. I was hoping there was a site like that! Now I just need to improve my kanji...

That was so helpful! thank you! Navtime can help you plan your trip in English too!

http://www.navitime.co.jp/en/