Disclaimer: I'm not an expert. I've built two ErgoDox keyboards in the last few months, but otherwise I have little knowledge of electronics. Having said that, here's my 2¢:
If the computer isn't seeing a USB device, I think it's not a firmware issue, but hardware. It's likely that your Teensy board is fried because of the short circuit you described. I recommend that you disassemble the case, remove any short-causing wires, disconnect the USB patch cable from the Teensy board, and plug the Teensy into the computer directly. If it doesn't see a USB device, the Teensy board is most likely fried. De-solder it from the main board and try again. In the meantime, get yourself a new Teensy board from pjrc.com. Wrap some electrical tape around the USB patch cable for good measure.
Maybe a real expert can confirm: if there *is* faulty firmware on the Teensy but the hardware is fine, will the Teensy board always show up as a USB device anyway?