[glend (Glen)]

So the camera works but just can't communucate via USB?
Now in removing the motherboard you had to disconnect the small USB connector board, I bet your problem is there, or in the small ribbon cable connection to the motherboard. It is easy to think that ribbon cable is connected when it is actually not fully inserted. Also check that the little earth bar is in place and has continuity.
They are pretty old cameras now, not worth spending money to fix them imho.

I would bet the camera did not need to be opened up at all, simply removing the battery and memory card for several hours would likely have reset whatever was hung. But yeah i suppose it is possible the usb board got fried by a spurious signal but it is unusual.

Finally, ditch the APT and use BYEOS, never had problem with that purpose built Canon software.