Controlling an Electronic Throttle Body using a PID controller

Trust me, I was against the idea of an electronic throttle body from the start (and I'm an EE!), especially because we have a cable operated throttle already. The ME's of the group insisted on using the electronic throttle body because they thought it would be easier than fabricating a throttle position sensor to a normal pedal that we can use to send to the motor controller. This way a commercial throttle pedal will control both the ICE and the motor.

At this point I don't have much of a choice other than to get it to work. If I shouldn't use a PID, then what should I use?

The throttle body doesn't have any control circuitry in it, just direct connection to the motor and two potentiometers that work inversely from each other. The throttle pedal has two potentiometers in it as well, but one of them has an extra resistor in series with it and instead of working inversely the difference of the two signals is supposed to be taken. I can't seem to find any documentation online about the system we have. All I have to go off of is this training manual we have. https://drive.google.com/file/d/0B7_wYqRQ2P5pT3l3RWhYRWpnaTA/edit?usp=sharing

In the manual there are no specific values listed, but a few plots of what the signals should look like and the pins we should use. Unfortunately though, it looks as if the ECU is supposed to do all the calculating. So I basically have to simulate that portion of the ECU with an Arduino.

With all the being said, do you have any suggestions as to how to control this in a better way?

Thank you!