Two weeks in Japan
Japan Rail Pass
Get a Japan Rail Pass  before you go.
To get it, you need your passport number, but the passport doesn't have to be physically present - this is useful if you're meeting up with people in Japan, as you can get theirs too. The passes only work for people who have a temporary visitor's visa - full visas and Japanese citizens are basically excluded (although check the conditions yourself as there are a couple of exceptions). You have to purchase it outside the country, and then obtain the actual pass upon your arrival in Japan.
It allows free travel on the Shinkansen or "new trunk lines" (super express trains - regular, on time and ridiculously fast), and is basically the price of a standard return ticket to Kyoto, so you start saving money pretty quickly. Not all trains in Japan are owned by JR, but JR offers the only nationwide rail network, and its lines run parallel (or at least close) to private railway lines in many cases.
A word of warning about the Japan Rail Pass. It is easy to fall into the pattern of hopping from one city to another after only seeing the downtown, main train station, and the most famous touristy spot. Slow down, spend some time in the city and the surrounding area, and don't end up spending more time inside the train than outside exploring the country you came to see.
Know the Station Names
If you are the type to plan your trip in advance, it may be helpful to write down all station names on a piece of paper. That way if you don't speak Japanese, you can always show the paper to the station attendant, and they will be more than happy to tell you what train to get on. Include all the transfer points too.
A great tool for planning your trip by train is Hyperdia. It'll let you exclude the Nozomi trains (which you can't take with the JR Pass), and limited express trains if you're going budget.
Japan has three main international airports: Narita (outside Tokyo), Kansai (outside Osaka), and Chubu Centrair (outside Nagoya). Most other major cities, including Sapporo, Sendai, Niigata, Hiroshima, Okayama, Fukuoka, and Nagasaki, have direct air service to the largest airports in East Asia. (Seoul is a convenient connecting point to these cities), but not to the Americas or Europe.
Most travelers arrive in Japan by air, but it is also possible to arrive by boat. The fastest boat to Japan is the hydrofoil from Busan to Fukuoka. There is also an overnight ferry service on several international routes: Osaka-Shanghai, Kobe-Tianjin, Shimonoseki-Qingdao, Shimonoseki-Busan, and Nagoya-Okinawa-Taipei. Ferry service is also available from the Japan Sea coast to Vladivostok in the Russian Far East.
Japan is a pretty safe destination for tourists. There are low levels of crime and you are unlikely to see many police cars during a two week stay. You should not need specific vaccinations before leaving your home, but make sure you have full travel insurance as medical care can be expensive.