Basically the problem laid all in the air pump. The relay and pump were bad so it kept running once the car was off. Not only did this kill the battery (was dead 4 times) but it also killed 2 alternators.
First I replaced the battery, and the car died again. Then I replaced the alternator, but the car charged at 12 volts, before I got a CEL and a BAT light. Then the RPM and volts started going crazy before I finally took it in to check for any shortages. They fixed it, now it runs good as new.

Thanks to my awesome haggling skills, and great mechanics heres all I paid:

$600 for new alternator (Labor was a bitch) and new timing belt. On top of that they gave me a brand new alternator the second time I brought the car in.
$350 for new air pump and relay for the air pump

And thats all she wrote, I got a brand new battery by taking advantage of the warranty (even though my car killed the battery).

All I can say is f*cking audis.

 

Sounds like you got a deal! If I didn't know better, I'd think the pump and relay were designed and made by Lucas. LOL. My 1998 A4 is my second and last Audi. Don't really need the quattro here in Phoenix and I bought a new Genesis Coupe with all the bells and whistles for far less than my A4 cost new in 1998! I still give my A4 kudos for style - even today it's a most attractive design for a four door sedan.