First, let me second what Sneaky's said already; go on the right day, and the "recycle stores" like Hard-Off and 2nd Street can have incredible deals (still kicking myself for not picking up an 80's Greco Thunderbird that I didn't pick up for ~$180 because it was missing tuners). That said, the selection varies widely depending on the day and time of year (go shopping on the week after New Years, or around May 5th, and you're likely to see a lot of empty racks). Of the two Hard-Off's in Nara, you'll want to go to the one in Nara city, near the Shin-Omiya train station, as their selection is much better than the one in Yagi. There's also two really funky recycle shops I'd recommend you check out called "Kaihousouko". There's one in central Nara, near Ninokuchi station, and one in Kyoto that is nice, but I think you have to drive to. Their motto is "We buy everything", and it's true; you'll find everything from Greco's and limited-model Fernandes shredders right next to fishing poles and Dolce and Gabana clothing. Again, their selection varies, but it's usually quite good, and well priced. Each Kaihousouko also has a theme for some reason, so they're a pretty good way to kill an afternoon, even if you don't buy anything. The one in Nara's theme is Egyptian/Mesopotamian, and the one in Kyoto's is Wild West.
Second, it's not quite as dense as Ochanomizu, but the Umeda area of Osaka has a ton of great shops, including the ESP Custom Shop, which has used gear as well, along with a number of Miki Gakki stores, which are good for used/vintage as well. I'm not sure how much they would buy your vintage Gibson for, but I do know how much they sell them for, and if they are fair, you'd get a killing, depending on the year and model. I had a guy offer me $1200 for my '64 Harmony one time, and maybe things have changed, but I remember when you could easily get one for $250 or so at any shop with vintage/used. Anyway, it's really easy to get lost in Umeda, so have a list of stores with you and a map when you go.
Third, sorry I'm late! I just joined the forum, so I didn't see this until now, but I lived in Nara for 4 years before moving to Osaka, so I thought I'd pass along some info, in case you were still around. Hope you get a chance to make the most of it!
Cheers,
A-Lx