@Woot....You will not be able to get a JR Rail Pass once you are in Japan. They are only available to foreign visitors. If you plan to use it half way through your trip then you will still need to buy one before you arrive. Whatever agency you buy it from will send you a voucher and you redeem it at a JR office in Japan. Check out this link if you haven't already: http://www.japan-guide.com/
There is a wealth of info on there including transportation info.
There is a wealth of info on there including transportation info.