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It depends which engine you have.
On V6's it is on the right hand side at the bottom rear of the engine.
You will need to remove the alternator and possibly the right hand engine mount to give yourself enough room to remove it.
Removal of the alternator requires the radiator support to be in the service position.
I'm going to assume you have the 30v V6 as that was the most common engine for your car. Alternator replacement involves the removal of the headlights and bumper, draining coolant, and opening the front of the car (it's designed to allow this - google "audi service position" to see how it's done). Once the car is opened up the alternator can be replaced, but even then it's not an easy job as the bolts are difficult to reach and it's a really tight fit. It can be done but set aside a full day if you're not mechanically familiar with Audis. At a shop I'd expect 5-6 hours labor plus the cost of the part. Do it yourself or find a shop that is known for working on European cars, but don't go to a dealer. You'll pay $500-750 at an independent shop, but I'd bet on $1500+ at a dealer.
With volt meter on battery start car and read voltage. When yo first put the meter on a full charged battery it should read between 13-15 volts. When you first start motor the voltage should go 3-4volts higher then when you first put it on. And then tapper down after awhile. If there is no voltage increase after start alternator is out.
The other bolt ( the top one ) is only accessable from the right front wheel well. I believe it is a 16mm. it is located in a small recess in the block that requires a flex joint with a socket, or if you dont have one a ring spanner. It is difficult to remove as the bolt is very long. This is not an easy job and the car needs to be in the service position,ie. the front bumper off and the carrier moved forward. the only way the starter can clear the frame for removal is by also removing the alternator. Go to this link for an excellent description of how to put your car in the service mode http://www.audi-sport.net/vb/a4-s4-forum-b5-chassis/62793-so-called-service-mode-how-get-anything-front-pics.html
For 2001 Audi A4 the fuse box is located on the left side of dashboard behind a plastic cover (for left hand steering wheel vehicle). On inner face of the plastic cover you will find the fuse diagram. But the alternator don't have any fuse! You can check up electrical connections. If you don't find anything wrong the alternator is out of order. Replace brushes inside, or voltage regulator (see picture below)!
4 - Voltage Regulator
Did they specify that both of those were for the A4 of your model year, or could one have been for the S4 (the twin-turbo version of the A4)? If they're both for the A4, I'd think that logic would dictate that the 120 amp unit would be for the 2.8L and the 90 amp unit for the smaller 1.8T engine. I'm not positive, and I've yet to come across discussions of this on the Audi boards, but that'd be my bet.
You may not have to dismantle the front, but it'll be a lot easier to do it that way. Go to google.com and search "Audi A4 Service Position" and you'll find some procedures that demonstrate how to open up the front of the car almost like a door, to have unfettered access to the front of the engine. It will make life a LOT easier, and it's very easy to do it, despite the fact that it appears to be a huge task. It's not.
THIS IS A BIG PAIN IN THE ****!!!!!!! i would definately reccommend getting the repair manual from any pepboys or autozone because there are several things that you have to do to get to the starter. This is to include taking the front bumper off moving the radiator and the front headlights forward, then taking out the alternator. All of which have little room to work in.