The public transportation systems for many cities, along with the Shinkansen, eliminates the need for most tourists to rent a car. However, some tourists may want to explore smaller towns or specific areas of Japan that are not as easily accessible by plane, bus, or train. Renting a car requires a few steps along with understanding the basic driving laws.  

Acquire a International Driving Permit (IDP)
Japanese law requires tourists to have a IDP prior to visiting the country and renting a car, It is a fairly easy process in the United States through AAA. The requirements are filling out an application, obtaining two passport photos, having a valid driver's license, and a $20 processing fee. Pay attention to how far out you can get one before visiting Japan. 

Secure a Car Rental
There are multiple companies to choose when renting a car. Toyota Rent a Car and Nippon Rent-A-Car are two rental companies with many options and locations available for a pick up. Prices for cars vary by size, location, days of use, and drop off. You should expect to spend $50 to $60 a day for a sub-compact or compact vehicle rental. 

Rules of the Road
In Japan, you drive on the left side of the road. This may be confusing for many tourists that are used to driving on the right side. You should follow normal driving practices such as stopping for pedestrians to cross and obeying traffic lights. If an action is against traffic law in the United States, it is probably against the law in Japan. Road signs in Japan are in Japanese and English. Some of the common road signs can be found here. 

Expressways and Tolls
One of the most convenient options traveling by car from city to city is using the expressways. They are similar to the multi-lane, national highways in the United States such as I-95 and I-85. The Central Nippon Expressway and West Nippon Expressway websites are great resources for planning routes and learning more about using the expressways. While expressways are a great way to travel across Japan, their tolls can get expensive. Tolls are collected between cities and can cost almost $100 each way. According to the Central Nippon Expressway website, traveling from Tokyo to Kyoto requires a ¥9,900 ($90) toll. Expressway passes are available offering a discount for multi-day travel across Japan.  

Tokyo is a huge city. When factoring in population density and land area, it is one of the largest cities in the world. Seeing all of Tokyo in one trip to Japan is an unreasonable expectation. It is important to narrow down activity options and think about what are the highest priorities for you. Making a short list will help guide you as to what area of Tokyo is the best fit for you.
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Follow the Narita Express 
One of the easiest ways to decide where to stay in Tokyo is to pick a stop along the Narita Express (NEX). The express train from Narita Airport drops passengers off at major areas of Tokyo including Shibuya, Shinjuku, Tokyo Station, Ikebukuro, and Yokohama. There are plenty of lodging options around these stations. Getting back on the NEX to take a flight out of Tokyo is also convenient when staying near a station on the NEX route. 
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Stay Along the Yamanote Line
One of the best JR Rail transportation options is the Yamanote Line that runs in a full circle around Tokyo. This line stops at over 20 different destinations including some of the biggest tourism areas. Staying near the line simplifies navigating the complex transportation network of Tokyo. You can easily access the Yamanote Line by stopping at Tokyo Station after riding the NEX from Narita Airport. 
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Pick a Neighborhood to Explore
There are a few neighborhoods that cater to nightlife, shopping, and other interests for tourists. Do you want to experience a bar scene and some night life? Shinjuku or Roppongi may be of interest to you. If shopping is a high priority, then you may be interested in the Ginza area. There are certainly benefits to staying in a particular place such as saving travel time and close proximity for carrying shopping bags. 

Other things to consider when choosing a location to stay is price, amenities, and even how many people are traveling with you. Also note that public transportation does not run all night long and taxis are expensive. Picking an area to make your home base can enhance your experience and allow time for more of your favorite activities. 
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Happy New Year everyone. I hope you had a nice holiday. I have combined the four part travel guide into an easy to navigate page on the website. If you have any questions or feedback on the guide, please let me know. I hope the guide is helpful for your next trip to Japan.