So after searching these forums I figured it would be easier to read from the Arduino's VIN pin
VIN isn't an input. VIN can be used to supply >7V to power the arduino through the on-board regulator or to power external hardware from the supply provided at the barrel jack. I'm not entirely sure what you were doing, but it is clear you were not using it correctly.
I'm thinking its measuring the voltage left AFTER the Arduino takes its own portion?
Sorry, but that doesn't make any sense.
Going back to the differential sensor you have, how have you connected it to the vehicle's battery? Do you have a common GROUND connection for all your hardware?