First, I set up a spot loader in the chunk I was using as my rail station. Rail station consisted of a module toggler, a cargo manager, some detector rails, and advanced detector rails. Two carts, one that only had an engine, track remover, and cleaning machine, the other had galgadorian drill, chests, bridge builder, height controller, and engine. Both also had chunk loaders. It was set up in such a way that when the drill cart returned, it would first pass by module toggler, turning off the drill and chunk loader (why waste fuel?), unload cargo, cross a detector rail, go around a loop, and park on an unpowered advanced detector rail. The detector rail was connected to the advanced rail with redstone, so the two carts took turns doing their thing. The cargo manager dumped the harvested stuff into pipes which trashed some, and sent the rest to my AE system via ender chests. Of course excluding the fuel, stone bricks, and rails.
There was also another detector/advanced detector set up with a counter (i.e. dropper-comparator setup) so that the whole thing would park after a given number of trips.
A track was laid to get the cart up to an altitude 9 blocks below the height of the village (because of the 9x9 footprint of the drill) and a detector rail was then laid down. The detector rail was just to stop the cart with the track remover from taking down all the tracks on the ramp, carts with height controllers can be weird about re-laying those tracks properly. I then ran the cart with the track layer and bridge builder so that it created an elevated track running the entire width of the village. Every 9 blocks I placed another stone brick with a rail adjacent to the first rail. Then I let the whole thing run while I went off to do something else.
The way it works is that after the drill/bridge builder/track layer reaches altitude, it will continue in a straight line, until it hits one of the spur tracks, then it will make a 90 degree turn, and continue on until it runs out of tracks, bricks, or storage. When it returns to the train station, the cart toggler turns off the drill so it doesn't wreck up the place, and the track remover is sent out. When the remover returns with a load of tracks, it dumps them in the cargo manager, and sends out the drill again. The drill loads up with those tracks, and more stone bricks, and repeats. Because the first spur track is now removed, the cart doesn't turn until 9 blocks later. The aforementioned dropper should start with 4x number of items as there are spur tracks.
Once it is all done, you have to repeat the spur track setup 9 blocks lower, and don't forget to reset the height controler, or it will all get mucked up. The good news is that it will tear down the previously placed stone bricks and put them directly into the bridge builder, so you don't really have to worry about running out.
If you find this description confusing, here is the original mining design that I adapted my setup from. Hopefully it will give enough insight to make sense of the rest of my description. I really need to finish building my PC so I can start making my own videos...
