I have all the information you need on that system. Went to school for it in 2003.
Both valves you talk about are PTV and FTV Pressure trim valve is on the regulator and the fuel trim valve is on the throttle body. One is on 90% if the time the off 90% of the time. Do you have access to the GCP software and can buss ECOM? Check for 2-3 pounds pressure while running at the regulator. Turn the key on without staring and slowly accelerate the throttle. Listen to the electronic throttle or governor control for grinding noises like gears worn out. You'll need to hook up the scan tool once you fix it to reset the adaptive learn and clear the codes.