I'm not sure how much work you've done so far to make you think that the microcontroller is the suspect but I'd take a step back and consider the things that are most likely to fail in a high vibration environment.
Check carefully things like the connector to board solder joints, joints on heavier components like the relays (check relay coil continuity too), check the grounding, follow the supply circuit through, cracked passives etc.
The micro will be pretty well protected from the outside world (unless you know that something nasty has happened on the 12V supply, eg. jump start), even then I'd check the power supply components first.