-If you do want to live in Tokyo - and it's understandable why you might - be prepared for sensory overload and confusion like nothing you have ever felt in your entire life. It's a routine experience to see 50 or more people cross the same crosswalk at once on a major street, at 1 AM no less. Signs for shops, bars and other establishments ascend the sides of buildings, and a nice cafe or shop may be on the 10th story of a building. If you are averse to crowds, noise or overwhelm, DO NOT live there. Of course, Tokyo is, well, Tokyo - there's no place like it.
-Research the district in which you plan to live. The districts can be very different from each other, and while one area may be pleasant and bustling, another could be an abandoned industrial wasteland.
-Of course, given the train system, your neighborhood may not matter much as long as you're decently close to a train station - which is a very easy objective. A neighborhood may not be pleasant, but given the country we're talking about, you don't need to be concerned about getting mugged.
-Don't bring very much, and expect to be cramped. ALL affordable urban Japanese living spaces are cramped. Period.
-The traditional way to have an inexpensive, fast meal out is to get a bowl of noodles. Noodle bowls - ramen especially - are the meat and potatoes of Japan. Keep this in mind when you're eating on a budget.
-Do your best to go somewhere with a decent Gaijin community, unless you're okay with being isolated.
-Japan is not all fuzzy lumpkins and happy yay. Actually, it's chock full of societal problems. It's not a place i'd want to live for more than a year or two.

There's plenty more where that came from, but your eyes are probably falling out from reading. :D