I've read through your edit...it makes sense, but I'm not exactly clear on how to execute that given the config of the board. Should I scratch out the board line between R13 and Pin12, replacing this by a resistor from the R13 / D5 junction and Pin12?It might have cooked U2 if it applied >12.5V to pin 12. Before fixing it, fire it up and measure that voltage. Also when you pull U4 manually jumper u2-12 low and high to see if the output changes (assuming pin 13 is low - OR gate..).
The rest should be OK but you don't know until you get U4 gone.
The voltage reg might not be happy now that I think about it. It won't mind short circuits / overloads but won't like being back-driven by a seriously failed U2. Just have to see.
See the edit above for a suggestion to fix the circuit until you rev the board.
Have fun.
Is it actually possible to scratch out a copper trace?