You're right, most used camera shops focus on small and medium format gear, but many do have a few LF models (and lenses) - usually not in the front window, but in the shop itself (usually towards the back). You'll have the most variety (and luck) probably in Tokyo. Kyoto has a couple of shops (literally), your best bet is to go to Osaka (30 min from Kyoto on a rapid service train, faster if you use the Shinkansen) and see what they have there (I've put a link to map that lists shops below). In all honesty, I don't know if you'll find any good deals, even if you can find what you are looking for. While you are sure to get good quality, you'll probably pay for it too.
While you are in Tokyo go to Yodobashi Camera (Shinjuku) - it's split up among multiple buildings, but the film section is on the ground floor of one of them, and you can pick up some LF film you may not be able to pick up anywhere else (including quickloads). The other Yodobashis (and in some cases BIC Camera) in other parts of Japan do not have the same selection as the Tokyo one. I've been trying to keep track of the places I've been to, here's a link to
my blog that talks about shopping for film in different places in Japan. I hope to do one on used camera gear shopping in the Kyoto/Osaka region sometime in the near future.
Here are a few links worth browsing. Most are in Japanese, you'll have to rely on Google Translate (or equivalent) to navigate through the pages. The JapanCameraHunter guide has multiple links you can follow also.
First of all, read all the three parts of this guide from Japan Camera Hunter:
Camera Shopping in Tokyo
Map Camera (Tokyo) - I've linked a page to a map of the store. They do have a selection of Toyo cameras for sale ranging from 200,000 to 400,000 yen (with lenses) - the prices seem high to me but I can't tell if they are new or used. Could be both.
Lemon Camera (Tokyo) I could only find LF lenses here.
A
map of camera shops in Osaka. I've used this map myself for camera shopping there.