Gotta figure out what part you trashed - though you really ought to be able to short the power supply out without damaging the hardware, since it's something you will often do. I haven't done it to the official boards (too rich for my blood), but I short clones any my standalones out all the time.
A short of Vin to anything else, while it's powered off the barrel jack or Vin will typically damage stuff. The 16u2 is usually the weakest link here, oddly enough.
You'll need to get better at your test lead technique to have any hope of figuring it out.