Scope, hopefully you'll have a chance to read this before you return but here's a bit more info for you:
Top 3 record areas that have
tonnes of stores:
- Nishi (West)-Shinjuku
- Shibuya
- Ochanomizu/Jimbocho
I agree that Disc Union is the bomb. I hit up the soul/blues Disc Unions regularly. Actually, you'll want to get off either the south or east exist of Shinjuku to find the Disc Union's there. All the stores (soul, jazz, rock etc) are around the same area. Once you find one, you should be able to get a map to the rest of them. But definately dont sleep on west shinjuku. The place is loaded.
On the chuo/sobu line from Shinjuku you should get off at Nakano, Koenji and Kichijoji. All three stops have about 5 - 10 record stores each to check out.
You really need to buy the record map book when you find one of these stores (it's about 1500yen). It's all in Japanese but once you ask someone to help you get your bearings you should be ok.
And if you go any further out into the sticks, then hard off can be a go sometimes (but you probably want a car for this).
Food wise, I just recently discovered an awesome yakitori joint in Shibuya. It's a two story place that'll be constantly full of salary men getting wasted after work. It's crowded and not exactly the cleanest place in the world. But the yakitori is outstanding and the beer is ice cold. Plenty of sake to be had too if that's you're thing. It's here
http://gmap.jp/shop-1147.html. The link is actually a map to the Hobgoblin (an Irish pub) but this yakitori place is just under the "R" of "The Renga".