Do you apply for a Japan Rail Pass before or after traveling to Japan?

Before. I`ve never done it, but if I recall correctly, you have to have proof that you`re a tourist.

yes Japan rail pass can (only??) be bought outside japan, as far as what my friends did. Basically, you can choose the validity of the pass. you can ask your agency/airline about the pass. My friend from singapore bought his for $400 and its good for 2 weeks. you can use the pass for all jr trains except nozomi :D

Well, if you are planning on living in Japan, a Japan Rail Pass is unnecessary, right? Also, can you use your driver license, say from Ameria to drive a car in Japan?

Yes, the rail pass is only available outside of Japan. You purchase a voucher which you then use to get the pass once in Japan.

To drive with a US license in Japan you go to Triple A and get the international permit which must be renewed every year.

Where's Triple A, is it in America or Japan? Also, all you need to bring with you to Triple A is your US license, correct?

It is that company with AAA stickers everywhere. I think it stands for the American Automobile Association. Yes, the United States and all you need is the license.

I'm confused by all these "prefectures" and "districts", and I've been wanting to work and live in Tokyo. So my question is, isn't Tokyo just one city, or is it just one big city where countless cities live within it? Am I in the right direction?

One city made up of many different wards. Kinda like Manhattan, Brooklyn and Queens are all in NYC. But Tokyo is a prefecture in and of itself. Kinda like how Washington DC is not in a state but Tokyo is nearly six times the size of DC.