I did a lot of the shopping on line before I went. The auction sites in Japan have a lot of stuff but don't ship outside Japan. Some stores also list used items on the web that you can reserve by contacting them. For new items, there are web vendors that are cheaper than most stores, but again they won't ship overseas. Generally, these web-based deals are available to visitors from overseas only if you have a reliable address in japan at which someone can receive the items. Not to mention the fact that reading japanese, which I can, is probably essential.
The one thing that is a good deal in Japan no matter where you buy, it seems, is the current line of Cosina manufactured Zeiss products. The retail price in Japan is generally 10-20% off what you see in the States. A ZM Biogon 25/2.8 costs 91,200 (just a random sample of one store), approx. US$797. The price at B&H is $US923. ZM lenses are starting to show up used now, and you if you go to a big camera store with a used department, you might just get lucky and find a deal on a superb lens that is for all intents and purposes new.
The L with that superwide is a sweeet set-up!!!