I used to LOOOOVVVVEEEEE going to Shibuya every weekend when I was in high school. There are still a bunch of guitar stores there on one side of the station (sorry can't remember which one!). Or just go wander around Ochanomizu - a whole bunch of stores!
This link should work for
TC Gakki there in Tokyo. They've got a couple of used Rics - looks like a 3001 and a 4001S.
Music Land Key in Kyoto used to carry Rickenbackers, but it looks like they might not be an official store anymore.