Yeah, I highly suggest not using a car, espcially in populated areas like Kyoto, Nagoya, etc. It's not easy to find parking, and if you do, it's usually paid parking, which cost a lot, as mentioned. Traffic is so-so, I think, depending on where you're at, but the roads look quite narrow, too, even for a freeway (expressway..).
The toll is about 700 yen in the Tokyo area, and I hear it goes up to 3000 in others, and on your (long) travel, you'll have to go though more than one toll gate, most likely.
Just take a train or a bus and relax, instead. The train system is quite efficient.
Keiichi