A couple things to consider when planning.
When looking at a map and measuring how far apart things are, don't ever estimate travel time like you are in the US. 50 miles in the US might be under an hour on the highway in a car and a couple gallons of not too terribly overpriced gasoline. And parking is usually free. But in Japan, there are no straight roads and no straight line between two points. The highest speed limit on the most limited access highway is something like 40-50 MPH. Gasoline is two or three times more expensive. And anything larger than a foot path is a toll road that charges about a dollar or more per mile of pavement traveled. Going between two points takes a long time and a lot of money. And parking fees for garages and meters are obscene and there is no free parking.
Public transportation is good, but just about every possible route of travel involves 20+ minutes of walking to get to and from a train or subway station. Wear shoes that are comfortable to walk in and clothes that you can comfortably walk in at a brisk pace (just short of jogging) for a half hour or more at a time.
A rail pass pays for itself on the third decent length trip. You don't get to ride the fastest bullet train, or sit in the fancy seats, but getting there in an hour instead of 30 minutes still beats the alternative. There are several different rail companies, and not all participate in the rail pass program, so don;t be surprised if you do get to pay for some local subway and train trips, but always ask the ticket clerk.
There will be places not served by public transit. You probably won't find a rail stop close to a highway parking/service area, where car clubs and racers gather. Or near some mountain road or park. Or close to a little tuner shop out in the hinterland, surrounded by rice fields. Having a local friend with a car comes in handy. Taking a lot of gifts for that friend is a good idea, because they will be doing you significant favors and you will owe them a lot.
Addresses do not have street numbers with sequentially numbered locations. Postal addresses are based on mail delivery from a central location within each little postal carrier route. Finding a place is not as easy as looking at the street name and number and saying it's down the street from another known location. Websites, the backs of business cards, and advertisements, almost always have a map with significant land marks and roads to show locations of businesses. Be prepared to be lost. There is a reason that everyone in Japan has those strange antennas on their car, they are for the navigation systems. They don't go out without one.
If you do not have a hand held GPS device, this is your excuse to buy one. UDD has map files that can be loaded onto GPS units:
http://www.uud.info/
They are not perfect. The maps are several years old (like there is no bridge shown between the mainland and Chubu/Centair Airport). You can't turn up the detail setting on your GPS all the way without blank spots in your map, because there is just too much stuff for the little GPS to handle. You can't type in an address and navigate like in the US. But you can mark a known point, locate a point by matching the image on the screen with the little printed map from a website or advertisement, or load in way points from a computer program. In the very least, you can walk around an area, without someone supervising you, and not worry about getting lost.
Kuro Neko/Black Cat is handy for moving suitcases and boxed items from place to place (hotel to hotel or house to house) when they are too big to carry on the train or haul. When looking to ship stuff back, check the post office first, they are the least expensive, but have size limits. Spoilers and grilles are too long. Wheels without tires are usually not too big, even boxed in a stack of four. They still have M-Bag Surface, and it's a lot less than air mail. Learn the size and weight limits, and shop accordingly. And remember that over stuffing a suitcase over the weight limit for the return trip can result in $500+ in additional luggage weight fees, and a burning in the stomach for not sticking more stuff into the mail for a fraction of that fee.
Now I want to go. 
