Charging help?

Okay, so on Monday I'm at the Topaco Lodge at the Tail of the Dragon. I go out to the car, fire her up and the battery light is on. I popped the hood, everything looked fine and I proceded to drive her. When the opperating temperature got to normal the light went away and all was fine. From that point on, every time the engine got stone cold the same thing would happen. Another side effect (initially not noticed) was that when the revs reached a certain point the light would come on. So, yesterday I tested the alternator when the light was on and it was indeed not charging like it should be. So, I put a Ford reman alt. on this afternoon and still, anything above 2,500 rpm and the battery light comes on. I thought it might be a glitch, but I also noticed that when the light comes on the lights get dimmer. Any clue what it could be?
 
Alright, Advance couldn't test the charging system b/c the battery tested bad. Last Monday I got a replacement one from Interstate...made zero difference. I then tested the system with an Audi too at work and it said the charging system wasn't working (duh!). So I haven't really messed with it since then. This morning I got to thinking... I had noticed some of the insulation on a couple wires inside the alternator (the ones visible from the front) were chaffed, showing bare wire. So, I disconnected the B+ wire from the alternator, ran jumper cables from my Sienna (known good charging system), turned off all consumers on both vehicles (so as to not over-run the Sienna's alt.), started the van and then the Pony....the light was off and my meter showed correct voltage at the battery. Me thinks me might have a bad alternator from Ford after all! Might this be an incorrect way to check the alt. on the Mustang, tho (sounded correct in theory)?
 
I've checked darn near every wire on the car...it started happening down in the Smoky Mountains and I thought maybe a little critter had gotten in there overnight and chewed on a wire, but nothing. I'll call my favorite Ford parts counter in the morning and see what I've gotta do to warranty this thing. I'm not too experienced on the inner workings of an alternator, but I'm pretty sure bare internal wires isn't a good thing. Plus I figured that when the Sienna was charging the system fine that the only link out of the system was the alt., which in theory would condem it.:shrug:
 
Here are the wires in question...

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I'm not sure if they were sliced when they were putting the case back together at the reman. place or what, but they sure don't look good...:nonono: