http://fordfuelinjection.com/?p=63
I would disconnect the battery ground and use a 12 volt test light. Put the test light between the ground wire and negative terminal. If the light lights unplug the voltage regulator and test again. On older Fords this was the primary cause of dead batteries. Otherwise disconnect one fuse at a time until you find the problem. A bad alternator can also cause a ground unplug it and try.
The regulator has to be grounded for it to work. I've had to sand the mounting surface to get them to charge.