...specifically Kyoto and Osaka, where there are hundred's of record stores, catering to all genres. I only had time to check out four of them featured in this video, but if you're a vinyl crate hunter, try and make time for more, I don't think you'll be disappointed.
The four I visited were:
Happy Jacks - / happyjackkyoto
Poco a Poco - http://pocoapocokyoto.com/
Workshop Records - / 474794205981870
Records Forever - http://www5a.biglobe.ne.jp/~forever/
...more on these, and maps in the video.
If you're travelling that way, pick up a handy Technlcs sponsored guide 'At The Record Shop' which lists most of the independent stores. In this video I've listed the prices I paid.
Here are some more links to research more before you go -
http://www.digitalaudioreview.net/201...
https://www.odigo.jp/articles/164-osa...
http://www.electronicbeats.net/city-g...
Happy hunting!