The stator makes an AC voltage, the rectifier changes the AC voltage to DC voltage and clips the peaks to keep it at 14.5 VDC and the capacitor acts like a battery maintaining the 14.5 VDC during the times when the AC current is less than +/-14.5V. The capacitor is able to do this because of the long discharge time that you tested for.
Since you appear to have a power problem, and you have confirmed the stator and capacitor functionality, the voltage regulator may not be working (particularly because of what you said about the 6VDC earlier.
Having said all that, I still have a feeling something might not be connected properly because the engine was working before she blew up.
The primer plug allows you to apply power directly to the fuel pump and doesn't rely on the sleds power generating capability in any way so all it really tells you is the fuel pump works.
The other plug you probably applied power to was the lights test plug. This plug bypasses the relay and applies power to the hood electronics (MFD & lights). I know that it bypasses the relay because I found out the hard way. So when you apply power to this it should power up your lights and MFD...not just flicker.
