TrigrH, you're clearly confused. If the answer to the second question is "no", then the answer to the third is also "no" and the answer to the first would then be "yes". There is no damage to the slot or PCB traces since only (<2mA) PCIe signal traces got shorted - not enough current to cause damage to slot pins or PCB traces!
There is either a buffer, mux chip, or redriver buffering the CPUs PCIe signals (and isolating the CPU lanes from the physical slot) and the MoBo is at fault, or there is not, and the upper PCIe lanes of the CPU itself are dead. You can't have a "no", "no", "yes" scenario in this instance, since there would be nothing to isolate the HSOp(12), HSOn(12), and HSOp(13) signals from the lane 12 GNDs – (the pins that were briefly shorted by a foreign piece of metal falling on them) – from the CPU if there are no buffers or redrivers on the CPU's PCIe lanes.
BTW, there is no way of running Slot 1 as a ×8 in BIOS, nor are any other slots able to be used for a GPU since there is no Xfire/Sli support, but the purpose of my post wasn't to find "a PCIe to use", as I could just run a ×8 card in Slot 1 (or use a ×16 card by isolating the last 8 channels with Kapton tape). It was to determine what to replace.