We have been offered by everybody to travel in Japan by rail+day tours. We are usually traveling with a rented car, anywhere in the world.
We are experienced travellers and in good health.
We have also figured, that a 2 weeks tour with a rented car, will be much cheaper then with a guided tours.
Any tips and info?

I don't know if it would be cheaper than a tour or not...rental cars are expensive here. Then again, so are tours. You could inquire to the usual international rental agencies like Hertz.

Be sure to be well covered by insurance...the last thing you need is an international insurance problem. Usually, Japanese rentals include basic insurance, but check to be sure exactlly what is covered.

Driving is on the left, like Britain. Signs are often, but not always, in English as well as Japanese. Like anywhere, navigation can be easy or difficult. You should ask the rental company about an English language navigation system equipped vehicle...much, much easier than maps. The vast majority of streets are not named at all, so navigation is unlike anything you are used to.

Driving distances in Japan are not so far, but time is longer than you would expect, so you would need to plan accordingly.

Anyone who drives the vehicle will need an international driver's license, available in the states from AAA.

Kim

I agree wiht KimJapan that you need to check into the total prices for rental cars and compare them with a package tour or on-your-own rail-pass travel. There are a lot of rent-a-car websites to check. But all I hear is that rental cars are not cheap, and neither are the toll roads that will add up to lots and lots of yen the more you travel. Also, parking is neither plentiful nor cheap. Finally, what more can I add? Gasoline is about 80-100 yen a litre, I think.

It depends on your itineray and where you want to visit. If you are planning to be in the cities such as Tokyo, Kyoto, Osaka, etc. the public transportation is terrific and less hassle in my opinion. I've lived in Japan 9 years and don't have (or want or need) a car. Day trips from Tokyo or Kyoto for example can be done just as easily by train.
Japan has fantastic public transportation that is usually on-time, fairly clean and quite extensive. In trains and stations you can usually come across very friendly and helpful people who can offer assistance/directions to some extent, although it won't be in flowing English in most cases.

If you are going to drive up northern Honshu, Hokkaido, or Kyushu for extended periods then a car wouldn't be a bad idea if it is cost efficient. Having the freedom of stop and go can be great in the countryside.

A little more about costs of driving...might be helpful.

Gasoline price is currently around 94 yen/liter for regular unleaded at a self serve station. Premium unleaded is about 125 yen/liter at self serve. Full service stations, which are by far much more common, are more expensive by about 10 yen/liter, sometimes more.

Tolls are outrageous...but I don't think about them anymore! There is a set price for travel per kilometer, as well as different calculations for small cars versus trucks etc. We have a regular car (which you would probably rent), and for reference...toll from Kanazawa (where we live) to Tonami...takes 20 minutes...is 1050 yen. From Kanazawa to Osaka...takes 3 - 3 1/2 hours...is about 6500 yen (give or take a few yen). From Kanazawa to Nagoya...takes 3 hours...is about 5500 yen. Bridges also have tools a lot of the time, especially in the bigger cities. They can be as cheap as 100 yen...or much, much, much more.

Of course, you don't have to use the toll roads...but, the non-toll roads are slow, slow, slow...lined with shopping centers and many traffic lights.

We are a family of 3, and for us, it IS cheaper to drive our own car for trips. The toll plus gas is about the same price as one person's train fare...so for 3, we really come out ahead.

Parking isn't so much of a problem. In the big cities, we use hotel parking, and though the posted price is quite high...400 yen/hour...the hotel gives a discount so we end up paying about 1200 yen a day. Once in the city, we leave the car in the parking and use the subway. Outside the cities, tourist sites and temples and so on have parking that is either free or quite affordable.

Often, you can get very affordable packages that include hotel and train/bus transport and leave you to sightsee on your own. This might be something you want to consider.

We've lived in Japan for 9 years too! But, not in one of the bigger cities, and we've found that a car is essential for us as our public transport isn't good in our city. In our case, we do save money by traveling by car...but ours is bought and paid for. Rentals...like I said, check carefully about the actual rental price and insurance, consider the tolls and gas like Babiron said, and consider whether or not you actually like to drive.

Kim

We drove around Kyushu and "trained" it everywhere else. Driving around and island meant you had to end up at the beach eventually even if you got seriously lost!
It was a highlight of our trip, although a little crazy in spots because you could do what you want and explore areas you couldn't get to otherwise. We wouldn't have been able to use the vending machines on the side of the road on top of high mountains while taking in the breathtaking views!
We purchased the Road atlas of Japan before we went so at least we have some English signage in the car. Go for it!