Okay I have the ball finding part figured out now.
Now I can't seem to get a valid PWM signal from the pins that aren't being used by the shield. I need them to control the motor controller. The sweep (servo example) code works fine with the same hardware setup and I have tried servos in place of the motor controller as well. I know the problem has to do with interrupts in the TVout library but I do not know how to work around this... Any ideas/ experiences?