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Might be low miles, but cables and grounds are 16 years old and probably have never been cracked open. They can get corroded badly internally depending on road salt. Try a "voltage drop test" on top of the others. I've read just 0.06 of an ohm (six hundredths!) resistance in the charging system will reduce alternator output by about 30%. Might not be "the" problem right now but could be the cause of it.
No. Under moderate loads the alternator is constantly turning off and on to avoid overcharging the battery. If left on all of the time it can lead to the battery exploding. Which I have seen first hand.
I don't think that such a repair would cause the concern you mentioned. The circuit is already hardwired to do exactly what the temporary jumper is doing, see the previously attached drawing. All the temporary jumper is doing is bypassing a segment that has started to fail due to a slight increase in the resistance of the wiring, slices, fuse link, or connector.
Restoring the wiring to it's original configuration is obviously recommended, but I do not see a situation where, in this situation, a dangerous condition might exist.
As a background, in the Conturd/Mistake/Cougar car lineup (I've owned Conturds for way too many years now), Ford issued a TSB (00-25-06) that explicitly changed the wiring as per my diagnostic suggestion as a permanent repair to address this exact concern. If your scenario were plausible in an instance such as this, I doubt Ford would have made it a recommended repair on that line. There isn't any particular difference between this charging system and that used on the cars of that time frame.
I don't think that such a repair would cause the concern you mentioned....As a background, in the Conturd/Mistake/Cougar car lineup (I've owned Conturds for way too many years now), Ford issued a TSB (00-25-06) that explicitly changed the wiring as per my diagnostic suggestion as a permanent repair to address this exact concern.
I just read the TSB. It does not appear to say what you think it does. It is relocating the sensing cable, not the field voltage supply cable. In that case what is happening is that the voltage regulator is reading an incorrect voltage and so the sensing line is changed. The alternator is still controlled by the voltage regulator.
Edit: Then again, maybe not. Looking at the diagram it implies that all of the field control is inside the alternator with no interaction from the outside. If that is the case then the line from the outside of the alternator is only a sensing cable, not for field control. If that is the case then applying 12V shouldn't be a problem as the voltage regulator is still actually controlling the voltage.
In a perfect world, you'd figure out the particular segment of the circuit with the fault and repair/replace that segment. Yo can use your improvised jumper to bridge segments and see which one has the high-resistance.
I've highlighted the charge-sensing circuit in the attached drawing. I'd focus on the segment that includes "Fuse Link C" as my primary suspect.
Thank you for the advise and directions I located a bad fuseable link and now the truck is running great!