1) The 0.5V probably comes from having the USB powered. The FTDI chip will be trying to put logic 1 on the RX pin of the ATMEL. That will feed onto the 5V rail through the ESD protection diodes in the ATMEL.
2) Not sure, seems like the ground track is broken despite your continuity tester.
3) Seems like the track from +12V to the regulator is broken.
Most likely the copper shavings shorted the 12V rail and the current from the PSU burnt the tracks away. Not sure why that isn't visible though. Possibly some vias have gone.
2) Not sure, seems like the ground track is broken despite your continuity tester.
3) Seems like the track from +12V to the regulator is broken.
Most likely the copper shavings shorted the 12V rail and the current from the PSU burnt the tracks away. Not sure why that isn't visible though. Possibly some vias have gone.