What brand alternator did you use? If not OE, Bosch, or Valeo, change it again.
Sorry for the late reply. just to go ahead and close this out, it was a bad alternator. Took the 400 dollar hit to my wallet and bought a new one. Spent a few hours yesterday replacing it. So far I've driven it about 30 miles without the battery light coming back on. Thanks everyone for the help.
Step up and buy a Bosch. Yes, they do fail, but the odds are much less.
Bosch is still the gold standard but not what it used to be. Don't buy cheap junk.
Stick with a high quality oem replacement alternator; VW installed a number alternator oem brands (bosch, Valeo, Hitachi, etc). My 2002 New Beetle Turbo S; had a Valeo 120 Amp unit installed, I had a hard time finding a Valeo unit, so I went with Bosch and so far, I have not any issues with it but the body of the alternator, was slightly bigger, so the wiring harness, was a bit of a tight fit.
I'm using a MK2 Golf alternator. It has the correct mount width, and has the right frame to mate up with the nice rack and pinion style adjustment bracket also from the MK2 Golf.
B5/5.5 alternators come from two vendors, Bosch and Valeo. I've heard they're not interchangeable because of different pulleys.
Mine has 69K miles. I've owned it for 4 years. Replaced the alternator and MAF sensor after failures. Keyless entry works only sporadically on the driver's door (lock switch already replaced - latch mechanism needs to be replaced, but for $$$).
I had a bosch alternator in my Mark 2.. 8valve motor. I noticed the battery was not being charged. so instead of dealing with the voltage regulator or brushes etc, b/c the unit was old I decided to go with a brand new one.
I when my original alternator failed in my 540i/6, the replacement rebuilt Bosch unit would produce 13.5-13.7v for a while after the car had warmed up, then would gradually fall to less than battery voltage. Running the A/C and revving the engine at stoplights would keep the battery light from flickering, but eventually, it would show full symptoms of a dead charging system.
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