Agreed on Expedia.
This will be my third trip to Tokyo in November and i've booked all three times with Expedia.
I really thought I wasn't going to be able to go this year due to the credit crunch...but the hotel I always use in Shibuya was doing a deal, stay 4 days and we'll knock 33% off you bill. 2 weeks booked on the spot
I find it's usually around ?2200 for me flights and hotel(but I do stay in a flashy hotel).
Food is cheap unless you act like a spanner and eat somewhere rediculous. I've eaten very well in Shibuya for a lot less than 4000 Yen a day.