You guys are making this problem too hard. I use the train to clean the track. I have recently bought a few hundred feet of used track that was slightly rusty. Before I connected the track sections together, I bent the rails where the pins are installed so that the pins were slight splayed. Holding the track section with the pins pointing away from you, grab the left rail where the pin is installed and bend it to the left. Then grab the center rail where the pin is installed and bend it to the right. Bend each rail so the end of the pin is offset about the diameter of the pin. Now when you connect two sections together, the pins will burnish themselves and the inside of the adjacent section. Now assemble a layout.
At this point, I put a loco and some cars on the track, connect up the transformer and run the train. I initially set the E unit for forward only until the track is clean enough that the E unit doesn't trip. If there are places that are not getting clean due to too much rust, I use the end of a tie as a scraper to scrape off the rust on the top of the rails.
After running the train for 2 hours or so, you will notice a very narrow shiny stripe on the top of the rails.
The last batch of track I did was quite rusty, and I had to clean out the open of some of the rails. I used a small rat tail file. I like John's suggestion of a small wire brush which can be obtained from McMaster Carr.
