Agreed with what Biggamehit said. Yahoo Auctions is nice. Upgarage has some nice stuff too. The closest one to you is the Kyoto Yawata Store about 6.2 kms from your school.
UpGarage Kyoto Yawata Store
Here is a map.
Kansai Gaidai University to アップガレージ京都八幡店 - Google Maps
You'll probably find nothing at a junk yard, cause all the cars you want parts for are usually snatched up at auction before. You can also shop on Upgarage's website, but you have to register first and their shipping rates are a little steep. If you don't read Japanese yet, it'll be challenging for you to do that.
However, Yahoo Auctions can sometimes have some pretty mean deals too...but you have to pay a monthly fee for the privilege of bidding on things over 5,000 yen.