Alright, I've been thinking and I am going to change the EGR control around a little bit. As it is currently I'm just adjusting the duty cycle to the EGR valve to control its position. However, when in use, there will be pressure pulling/pushing the valve and its position will be unknown. However, the engineers in their ultimate wisdom added a position sensor to the EGR valve so they can tell the position of the EGR valve. I will now be modifying my circuit and programming to get feedback from that position sensor and adjust the PWM accordingly to maintain the set position.
Here is the pinout/circuit for the EGR valve:
