2006 Focus 2.0, Ford "Smart charge" out smarted alternator into not charging?

Joined
Sep 23, 2008
Messages
13,359
Location
Ontario, Canada
These cars use Ford's first smart charge system introduced in 1999 on many/most Fords.
It seems my ECU has given up on running the alternator, with the alternator gradually not charging over a long drive home. I've read that pulling the 3 wire controls plug is the way to diagnose if the alternator is working. That plug is quite difficult to get at on the side of the road, so I did the easiest option and pulled the voltage sense fuse, and the alternator started working again.
Since I pulled the voltage sense fuse the alternator runs pretty much perfectly! With the exception of not charging at low idle when the car is warmed up, and I get the odd very short voltage spike to 15-15.5V just as the motor spins up off idle, but not every time. I live in the country and its a manual so I rarely idle anyways.
I have a ultragauge so I can see what voltage is, in real time, and it pretty much does what you'd expect for a healthy charging system, other than the idle drop and odd spike.

I've been running it like this for a couple weeks now with no problems, but has anyone run a ford with "smart charge" for an extended time in default/dumb mode without an issue?
Battery is new, and charged, charge cable and battery ground are good, so I think it is the ECU, but otherwise the car runs great and I will run it as is, if its not likely to fail?
 
On my 2015 Ford Focus, I located and disconnected a connector plug attached to it's negative battery wire a few inches from the battery terminal. I reset the battery programming with 5 high beam flashes while holding the brake pedal down. No more battery at 80% or less all the time. The battery stayed fully charged every time I checked it in the mornings.
 
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