I've been reading here for a few weeks, just signed up.
This issue has been a problem for my '03 and 06 Superduty trucks for years.
The first thing I noticed way back when I bought the first one in '03 was that battery voltage seemed to be low all the time, at least compared to my '95 model.
The truck came with a single 105a Alternator about the size of a softball or so.
I had bought the truck to pull my trailers, both a small equipment trailer/car trailer and an enclosed car trailer.
Both have various accessories powered off the accessory trailer port, including both having onboard batteries that needed to be charged while in tow. With in a few months of buying it died on me on the road. Still under warranty they replaced the alternator saying it had 'burned up its diodes.
The new alternator didn't last but another week, leaving it dead in my driveway. The dealer installed two new batteries, an alternator and told me all was good, this became the story for the next four years. Checking it myself I noticed that it never charged above 13.4 volts or so, and that dropped to 13.1 with the lights on and 12.7 with the trailer on and lit up, and it dropped to below 12.5v with the brakes applied when four trailer brakes were active.
I take it back in for warranty and they tell me maybe its my trailer, so I took it in with the trailer, they tell me that its not designed to tow a trailer with an onboard battery and such a major demand, in short they blamed the trailer,
I borrowed a new trailer, a basic landscape trailer that my buddy had just bought and it did the same thing.
Keep in mind it never did blow the trailer or charging fuses that fed the trailer plug. The truck at this point still only had about 4k on it since it got used only to tow toys around.
This went on for 8 years, meanwhile I got the chance to own the 2006 model that belonged to an uncle who passed away, same motor, same configuration, same alternator. Same issues. I basically gave $5k for the truck which was then 6 years old with 900 miles on it at the time. It had sat for a few years since he hadn't driven in a while so I had to buy two new batteries and new tires for it but it was garage kept, as was my '03. It had never had an issue and had never been back tot the dealer other than for oil changes. It barely made the 300 mile ride home. I got back home with a check engine light and alternator light on the dash and a truck that wouldn't idle.
Still under warranty, it went back to the dealer, but the dealer here refused to work on a truck they didn't sell, seemingly pissed off that I had bought one elsewhere. I had to take it to a dealer 50 miles away.
It got towed there, and the other dealer said that it needed an ICP sensor, and that they were going to update the fuel pump and perform 9 recalls that hadn't been done on it. Then they said the alternator had 'popped' its diodes. so they replaced that too.
They had it for a month. I picked it up and was charged $100 deductible.
I drove it home, and didn't get 20 miles before it shut off on the road and had to be towed back to the dealer.
They get back to it the following Monday and called me telling me that the fuel filter was clogged up causing the pump to starve for fuel. The truck at that point had only about 1,200 miles on it and the only fuel in it I put in it at a fuel stop on the turnpike. They charged me for a fuel filter assembly and filter, $1,400, and I picked up the truck, it didn't make it out of the lot before it shut down. A tech came out and said its got an ICP sensor code. After a week, they called me and told me the new ICP sensor had failed, but don't worry, 'It happens' and they were going to cover it. Week three, I pick up the truck and it won't go over 40 mph, so back to the dealer again, this time they tell me an o ring failed in the new pump assembly and that too was under parts warranty. Week four. They call me and ask me if it was okay for the service manager to drive the truck a bit to make sure it was really fixed. Two weeks go by and the service manager calls and asks me if I had charging issues in the past, I reminded him that it was the main reason I took it there a month and a half prior. He tells me that the alternator, wasn't 'commanding' enough amps to the batteries and that over many miles, it slowly lost battery voltage and wouldn't start. They had the truck for 6 more weeks, they got the factory rep involved and even offered me a loaner car. They ended up replacing all the battery cables, the engine compartment harness, ECM, the trailer connector, and both batteries and the alternator again. The manager again said he was going to run it around for a week to be sure it was fixed. It wasn't.
Ford had authorized converting it to a dual alternator set up and they went ahead and did that swap, so it then had two of those mini alternators and the wiring that goes with them. But it only prolonged the issue. After nearly 3 months Ford says to replace the instrument cluster because they found a ,21ma draw on the system when the truck sat. They give me back the truck finally saying its all fixed and that I won't have any more issues. They 'wave' the additional deductible. They had the truck for four months and a week, and put 230 miles on it.
They even did an oil change because it was required after the ICP sensor and/or pump failure, twice.
The truck sat most of that winter, being used only a few times a month. I found it too discharged to start after sitting about 7 weeks one day, I charged the batteries and found it charing only at 13.5v, and it basically did the very same thing as my '03. I call the dealer and they tell me that 13.5v is perfectly fine and there's no problem. But if it sits for more than a week it won't start. The draw on the thing, which is minor, and half of what the draw on my car is, take the battery voltage down to only 12.6volts and it doesn't have enough reserve to start the engine. The same crap as on the '03.
The 03 meanwhile was going through batteries and alternators too, I was getting maybe 500 miles out of an alternator and a year tops from the batteries. After alternator #7 burned out, I found all the videos that were popping up online about these trucks having charging issues, just like both of mine were having.. I took the advice of several on Youtube and said screw the warranty and bought a new super duty 3g large frame alternator, which was basically what was OEM spec for the pre-1997 models, and I bought an aftermarket voltage regulator that took the charging control away from the ECM. Amazingly the truck suddenly charged the batteries at 14.4v and stopped burning up batteries and alternators. That was back in 2018, and its been good ever since. A few months later I did the same thing to the '06, on which I hunted down the single alterator wiring and bracket and converted it back to a one alternator set up using the same 3G alternator and regulator with two new batteries. It too has been perfect since.
It turns out that smart charging on these really isn't controlled by the ECM, the alternator is just crap and undersized. with the glow plugs on, which they remain on for up to a minute after it starts, the alternator has to supply over 140 amps to maintain a charging state., if not the batteries take the brunt of the load and if the truck isn't driven for several hours after each start the batteries constantly lose charge both killing the batteries and causing the alternator to work at its max output just to try and recover the batteries from each start.
Since I generally only drive maybe 20 minutes at at time, it never had the chance to fully recharge. Adding in a trailer and more load only made it worse. With the alterntor swap and two additional battery cables to the batteries, the 03 has now got almost 18,000 miles on it with no issues, and the '06 just turned over at 40,000 miles with no more issues.
The trailer wasnt the problem after all.
The way both of mine work is that the only part of the truck's electrical system thats required for it to charge is the completion of the charge indicator lamp circuit in the dash when the key is on, when the key is on, it sends 12v to the regulator 'waking up' the alternator. After this function also shuts down the alternator to prevent any draw from the alterntor when its not running. Jumping this wire to B+ will effectively make it a one wire system but will put a small parasitic draw on the batteries. I chose not to do that but they do explain it in the new alternator paperwork.
I won't get into which brand alternator I bought, I doubt that matters much but I did change out the original voltage regulator that came with the new alternators for one that was made in USA, this change gave me an added .3v to the output. Now after a cole restart, it recovers its battery voltage fully in about 20 minutes and brings the batteries to a full state of charge in about 40 minutes or so even after a cold weather start.
