Replacing the Voltage regulator of a fried Arduino
I know it's an old thread, but others are likely to have this problem.  If you check the open source schematics, there are a couple of nearby capacitors that connect pin 1 (GND) to pin 2 (+5V) of the regulator.

I would check C2 and PC2 (top right of the diagram) as well as C1 (top left of schematic diagram), and any other components you can find that bridge the rails between +5V and ground.  Capacitors are more likely to fail shorted than many other components.  You will have to remove at least one pin of each capacitor to test it since you don't know where the short is, or you can simply remove capacitors until the short goes away.