The Akihabara one shouldn't be hard to find. It's a big black building on a street corner with multi-level pop-culture madness.
The Shibuya store is in the basement of the BEAM mall, however keep a lookout for the sign/logo on street level.
The Nakano stores were a pain in the arse to find as they were inside a mall and up on the 3rd floor or something. However it was closing time and I was in quite a rush.
There's better stores in Akihabara but most will take effort to find, which may not be fun if you're travelling in a group.