to me your micro usb daughter board still looks like it does have a ton of chafed wires, that could all be causing your short, have you tried to measure from the pins with the board unplugged, i am still rather very suspicious of it and before going for a full conversion we may be able to salvage this one. and if those 2 resistors read 22 and your schematics are good then a dead short on the UC side would read 44 ohms, so it kinda rules out the UC as being the culprit and instead something before those 2 resistors.
part of me thinks that the best course of action would be to to de-solder those wires from the usb board, cut the currently exposed part, strip a bit of the insulation off, tin it before they start chafing again and solder them back on, and given the quality of the wires, maybe add a bit of hot melt glue before final assembly, as a stress relief
oh and if this photo is before repair then disregard the repairing the daughter board, if your wires do not short like that anymore i suspect that it is just trash (the usb board, either internal failure of the pcb, or connector)