Thanks for the response David, and great to see you're looking into the problem.
To make it clear, the shield wasn't hooked up as displayed in your picture 
As stated in my earlier post, the following wires could have touched (although not with the VIN)
2 wires (TX and RX) on the OBD2 Shield
1 GSM TX wire on the GPRS shield
2 wires (SCL and SDA) on the GPRS shield
I also don't see how something else could have short circuited the VIN.
Power was supplied by the cars battery through an OBD-II cable (12V using pin 16).
It won't have been a clean 12V, as it depends on the state of the car (driving / stationary) and the battery (fully charged or not). When it blew the car was stationary.
AFAIK it will have fallen in the supported input range.
The OBD-II shield that was connected with the OBD-II cable delivered that12V input directly to the VIN of the Arduino board (thus also powering the grps shield).
Again thanks for taking the time to have read my post and following up on it. Really appreciate it !