2003 Volkswagen Passat Battery/Alternator/Computer Problems

Long story. 2 weeks ago while driving, my battery and alternator light came on. Also, the MFD displayed "alternator workshop". I took it to a VW dealer. They said I needed a new battery and a new alternator for the astronomically high price of $1600. I went to Pep Boys instead who quoted me $600 for the same work. Pep Boys however determined that I did not need a new alternator. Just a battery. So they replaced it. A few days later I was driving home from work when numerous electrical issues arose again. Battery light came on, airbag light came on, abs light came on, MFD displayed "alternator workshop". Also, the radio turned off and on, and the car beeped at me several times. All these problems occurred primarily once I hit 40-50mph. After I got where I was going, I turned off the car, but it wouldn't start. So I got it jumpstarted. I continued driving. However the car was now lurching and threatening to stall. Sure enough it stalled. I had it towed to a different Pep Boys. This Pep Boys said I did need a new alternator. So they put new one in for $650. However, car still has same electrical issues going on (numerous beeps, warning lights, etc.). We took it to VW dealer and they ran quick diagnostic check which they said indicated that Pep Boys installed too small of an alternator. Pep Boys disagreed. Pep Boys took a look and determined that they installed the exact same alternator as the old one. Pep Boys says its a computer problem that VW must resolve. But Pep Boys also double checked the new alternator they installed just to make sure it was not a bad one. It tested out fine. I'm beginning to think there is some strange computer problem going on that is causing all these warning lights to beep and light up. Maybe that means the car did not even need a new alternator and battery?
Can someone help explain? Much appreciated, Dennis