It's not everywhere that you find European chess sets sold around Tokyo. But over the last 2 days I found a couple of places near where I live. One joint basically sells all kinds of wooden toys, while the other is a sort of general store (called "Village Vanguard") for knick-knacks. I was even pleasantly surprised to find the same glass chess sets that Chess Discount Sales once gave away in some tournament (I think the SIO) being sold around here for a very cheap 1,000 yen.
For serious tournament players, the local JCA seems to be the only retailer of popular programs like Fritz or books and boards. But in my case, I have no worries. I pretty much packed all my chess software, a digital clock and a couple of boards when I left.