If you haven't done so already, I would get your hands on a Ford wiring diagram.Get the good ford book that the dealer techs use, not the garbage CD's on ebay or the piece of shit discount auto parts store shop manuals.
Second on a 2001 Cobra for example, there are two wires going to the starter relay. One is a white pink wire going to the control circuit of the starter relay that is hot in start. A second wire is a light green violet wire that is hot at all times is the power, work circuit. You should see power in the white pink wire going to the starter relay in the start position. The light green violet wire going to the starter relay should have power at all times.
I would check the voltages at those points to narrow the problem down.
I guess I'm not sure if I've already stated this in my entire thread, and not trying to be a dick (probably just frustrated with the car), but I've been through the entire starting circuit. I have the big manual for this car. I appreciate everyone's help, but unfortunately, everyone here is wrong and I'm going to find out why when I leave it at Brad's for them to tinker with it.