Beware, the industry standard pinout for CAN on DB9 connectors is different to what Sparkfun use on their shield:
- pin 3/5 https://www.sparkfun.com/datasheets/DevTools/Arduino/canbus_shield-v12.pdfCAN bus shield schematic
- pin 2/7 (Vector tools for example).
Which software have you been using on the Arduino? Any additionnaladditional info on the ECU you're using, and the wiring in your system?