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I have a 2006 Explorer Limited 4.6 V8 that keeps popping up a battery indicator on the message center. I can clear it by pressing "reset" but it comes back, sometimes within a few minutes, sometimes not at all. This mostly happens in stop-and-go traffic in town.
Battery is new-ish (Motorcraft about 2 years ago).

Funny thing is, when I start the car, it shows 14.6 volts with headlights on and A/C. Then as I drive around for 30 or so minutes in stop and go traffic with headlights and A/C on, running errands, shutting off engine between store stops (it always starts just fine) I see the voltage drop slowly until it get down to about 12 V. If I then take it out on a long high speed drive 50-60ish, it will show a charge of around 13.9, as long as I'm driving at higher RPM steadily. But by the time I pull into the driveway again, it's down to around 12V again. So it seems to be charging yet, but just barely I guess. It's showing a P0260 Code. (Using Torque to monitor voltage while driving.)

So I've had it diagnosed at a Quick Lane store and they said needed a new alternator. Ok, no problem. $650 for a rebuilt Motorcraft after install.

I've been looking at other options. I have the wiring diagram for the vehicle and it shows three wires going to the plug on the alternator, along with the heavy gauge red wire from alternator to the battery. The three wires are red, green and yellow. According to the wiring diagram, the green wire that's missing comes off the middle terminal of the plug ("S" on the diagram), then circles back to the alternator to another post marked "S". But this is for the 4.0L only according to the diagram.

That's where I ran into the question. Mine only has two wires; red and yellow. Red supplies 12V and yellow goes to the PCM. The green wire shown on the diagram seems to indicate it's is for the 4.0 motor only. I've looked around to see if the green wire got disconnected but no sign of it. It's been this way since I bought the truck 5-6 years ago and never had any trouble w/charging till now.

I want to be sure the alternator I get is made to work with this charging system. Is anyone able to give a quick visual verification on their own 4.6L Explorer so I know I'm not missing a wire?

I've heard of reman'd alternators that don't work with the Ford charging system and just want to be sure I'm getting the correct one. I've spent a few hours researching and looking at youtube videos and websites and have found differing setups for different 2006 Fords but nothing specifically for the V-8 4.6L alternators.

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