Personally if you go to all the major retail places in Japan, I doubt you'll find too many deals much better then the US (comparison to B&H only for me ').
On the other hand, if you do know where to shop, then you can get most items a little cheaper (for me it's substantial compared to Australia prices).
From my last check, the 1Ds III is still at 799990 yen or there abouts, so likely you can find it at some places for around the 760000 yen mark.
I can't be sure on the rest of the stuff in your list, except buy your gear from Fujiya in Nakano if you're in Tokyo area, they've been the cheapest for me when I'm over there. ^_~