Both abmj-jr and guru have given some great suggestions here.

Check the sticky at the top of the thread for easy to find links to threads answering many of your questions.

For great deal gourmet lunches there's this fine one:
http://www.flyertalk.com/forum/showthread.php?t=468207
(you can often eat lunch for a fraction of the cost of an evening meal at the same restaurant - and the meal is often just as good)

If you're around Shinjuku you can get a wonderful evening meal here:
http://www.flyertalk.com/reviews/rev...?review_id=181 (the link includes a map and a photo of the restaurant)

To get the best out of your budget, eat your main meal during the day at lunch time (strangely, seemingly 'expensive' places like Ginza can offer the best value - restaurants practically fall over themselves to get Japanese workers to eat their lunches there and there's stiff competition.) Many places will offer delicious 2 or 3 course menus for 1,000 yen, sometimes less. You'll get tea or water included in the rate. Avoid buying beer or soft drinks with your meal (unless it's included in the rate) one drink may double your bill. Don't buy wine under any circumstances, that could triple it!

In the evening, focus on eating at places like noodle restaurants. YOu may need to learn the characters for Soba, Ramen, Udon, okonomiyaki or anything else you're particularly fond of. Otherwise, walk around until you find somewhere you like the look of, check the menu for prices and give it a try. If you look near rail stations, you're sure to find somewhere good and cheap (this is not advice I'd give to anybody visiting Europe!). I'd strongly suggest joining a queue if you find any, queues form at good, reasonably priced restaurants (or faddy new ones... especially 'just opened' ramen restaurants)

One last thing... please don't go up onto Tokyo Tower.
It's overpriced and, for almost everybody, extremely dissapointing (I've even been told depressing). If you want a great view, get one for free up the Tokyo Goverment Metropolita building in Nishi Shinjuku. Seriously, don't go!

Have you decided where you'll be staying yet?