Nissan Repair: Battery and Brake Warning Indicator short, 2003 nissan altima, defective alternator

Question
I have a 2003 Nissan Altima 3.5 SE. Recently the alternator went out on me. I replaced it with a refurb alterator from Advanced Auto and also replaced the battery. It was a nightmare. The alternator is in such an hard to get to place. I had to take all sorts of stuff off to get to it from under the hood and remove it. I also had to take off the front right side tire and flap to get to it. At any rate, I have replaced this and now I seem to have developed a short in the wiring system somehow. Each time I drive it now, the brake light and battery light on the instrument panel will flicker, then it will go off for a while, then come back on steady, and then flicker again. There is no pattern. I have driven it when it did not come on at all, and I have driven it when the lights never went off, and would flicker. There is obviously a short somewhere. Since I don't have any sort of manual that goes into the electrical system, where should I start? I know that I can fix this, but I just have no idea where to start.

Answer
Shannon,

Take the car to Advanced Autoparts and have them check the charging system.  I think you have a defective alternator.  Yes, I know you just replaced it but it sounds like the internals are defective.  Basically, this is the internal voltage regulator.  I do not think you can get it to get these lights to come on and off by wiring it wrong.  If the parts store puts their test gear on they can verify.