[janita]

Well, thanks for all this information.

We are going by car because it gives more freedom. If we would stay 50% of the time or more in big cities, we wouldn't rent a car, but we are leaving tokyo the moment we receive the car (first spend 2 days in tokyo without a car) and return the car the moment we arrive back in tokyo.
I'm pretty sure we can do most stuff by train, but i believe it's sometimes easier by car.

About the no drinking, no driving rule ... I don't drink ;-) and i'm pretty sure my boyfriend also won't drink the day he's driving, so that's not a problem.

We are watching for using our gps system from belgium and buying a japanese cart. Like this we can have the information in our language or in english.

@Nyororin : in my google maps it isn't noted down how much the fees are for highways. I see that the green roads are highways and the yellow aren't. And when i type from "tokyo to kyoto" (just to give an example) google maps is telling me we have to pay a fee but it's not telling me how much.