For the moderators, it seems reasonable to move this thread to the auto section. I was just asking about what electrical probes to use, but it has clearly expanded beyond that scope.
I do appreciate the suggestions and hopefully I will answer the recommendations below:
Window needs to be reprogramed: The window works perfectly using auto up and auto down when it's working. This shows that the window programing is correct.
Using the OBD2 port to see if there is a fault: I am using FORScan. This is a very powerful tool (far exceeds most OBD2 scanners) to evaluate my truck. There were no codes or issues seen, I also used this to reset the the Body Control Module (BCM).
Window not receiving Key On Command, looking at the diagram the Key On Command is tied to all the windows. So they should all work, or they all will not work.
From what the wiring diagrams show. The BCM only passes line voltage to the window switches and window motors. It looks like there are logic circuits in the master window switch (I already replaced this with a OEM Ford part) and/or the front window motors (the rear window motors are "dumb" only have 2 wires, do not have 5 wires like the front motors).
I just made sure the front window motor has a solid ground (sanded off paint under the connection). If that doesn't work I will start to probe wires.
So... does anyone have a suggestion for insulation piecing wire probes