Welcome to FT.

First things first - I recommend that you read the thread: "Japan (Tokyo and beyond) Master Thread"

In that thread, you'll find links to some useful information - such as how to find train timetables. (Answer: On a web site called Hyperdia). Once you've looked there, you'll probably find answers to most of your questions. If something still isn't clear, that's the time to add a question to an existing thread or start a new thread.