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I am not much of electrician, but don't think so. Shortening the control wire would turn the light on per my memory. The alternator feed wire likely has the fuse on it.
Now the big cable is directly connected to the batteries and shortening it would cost some serious problems, but you would smell it.
If it's anything like the 6.0L, one of those wires is the alternator sense wire. If it were shorted I doubt the regulator would field the alternator and you'd get no charge. The other wire is the I wire. It "switches" the alternator on, and also serves to turn on the warning light if necessary. If it were shorted, I think the warning light would be on, but I'm sure the regulator would again not field the alternator and it wouldn't charge.
The big wire is the B+ (alternator output) wire to the battery. If it were shorted, fusible links would burn, or the whole thing would burn.
Chamberlain......I was driving down the road one day and the darn thing just died on me. No power...nothing. It would start up and run for about 5 seconds and then do the same thing. I jiggled the wires on the plug in part to the alternator and then it started and ran all the way home.
I had changed the alternator out several weeks before and noted that the wires from the plug looked to be in distress, but left them as they were.
Do you think when I put some slack in those two wires and the truck started that I solved my problem? I haven't taken the truck back out because I am afraid it will die on the freeway and that would be really bad.
I'm not that familiar with the 7.3L. I do remember once with my Dad's that when a power wire in the trailer plug was shorting to ground that it was killing the engine. So maybe something like that was happening to you, a power wire was shorting and killing it.
I think I'd replace that pigtail at the alternator. I'm pretty sure that you can get a new one from Ford.
Also, there is a 99-03 7.3L Diesel forum down the page. If this is a common or known problem, the people down there will know more about it.
I believe diesel uses the same alternators gasers do.
There is no easy way the alternator small wires can get grounded, what would make me suspecting the alternator itself. I had lot of troubles with my rebuild alternator that was acting for 3 months, still passing bench test till it finally gave up.