Hi, i have just read through the whole of the thread regarding your battery problem. We are specialist in the field, having a BEng in Electronics and having worked in the rally industry for a good few years. We have come across this problem before, here is what you need to do/have done:
1) Look at the grounding points scattered around the vehicle, check the cables using a multimeter. Unscrew the ground points, clean the terminals down to metal and do the same where the terminal mounts. You'll notice that the terminals in some places mount onto paint work. Rub the this area down to bear metal, remount ground terminal and copper grease over it. Check the resistance between each ground point and the negative side of the battery.
2) Using a Oscilloscope, we use a Fluke 124 and a Picoscope Automotive, check the battery and alternator. These vehicles have a smart charging system as rightfully mention previously by someone on here and can ONLY be checked using a scope and someone who knows what the scope should be reading. Use the scope to also check if there is any ripple leak out of the alternator. This is very important as any AC voltage in the DC line will cause gremlins to be blunt.
3) I would also check the demister circuit for a short or a large current drain.
4) The charging system is controlled by the engine control unit (ECU), which should be checked by Ford and software flashed if needed. This is a common fault, as the software used by Ford is somewhat........well, it speaks for itself!
Let us know on here how you get on.
Enginostics
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