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Check for cracks or air leaks. These can cause hum/whine/whistles. Spay soapy water solution on the manifold at joints. Avoid spraying anything electronic directly. If the noise suddenly stops, you have found the air leak.
Sometimes the IAC valve can cause a whistle sometimes resembling an airhorn. Does the truck have a rough idle? With it having an emission leak code i would assume that you probably have a hole in the rubber boot that goes to the PCV valve located in the passenger valve cover. There is a plastic tube that runs from the back side of intake behind the throttle body to the valve cover it will have a rubber elbow on each end of it. Look at the end behind the throttle body. It will probably resemble this.
Ur power supply board is where the whistle came from.
Open the back cover,take a screw driver back handle taps all the transformers, so all the gaps pockets in the transformers clear up.The whistles will stop.
There is an obstacle in the scanner path, or the scanning head guides got bent (unlikely). There could also be something in the rubber drive belt driving the scanning head gears. Try looking inside with a light and check for scratches on the guide. Unfortunately, to fix the problem you'll have to either send the scanner to maintenance, or to open it yourself (voiding the warranty).
Can't be certain from the description but the cut wires might well be vss (speed sensor). If so, this can cause several serious problems with your system as the vss is a major input for both engine and transmission control. The speed sensor mounts where the older models speedometer gear/cable would have been.
Just a thought- remove the oil filler cap when the whine is present - (this checks if PCV valve is faulty, causing high crankcase vacuum, which in turn causes a whistling/whine noise as air leaks past engine oil seals). Worth a check.
Try listening with a short piece of hose pipe to locate immediate area/source of noise.