All the pins should be programmable to suit the vast majority of devices to program or read. For example each of them can be either VCC, GND, Data pin, input pin, output pin, Program Voltage pin, etc...
As shown on the self-test screen, from #4, #5 and #6 has a problem. Assume # means number or Pin number, trace all those where the traces are lifted or shorted, also check the VIA traces etc...
Can you take a photo of the traces you mentioned in your post "moved away from the motherboard"? What exactly do you mean?