Key fob works to set the alarm. Car chirps and the red light on the drivers door blinks. I assume it's set, but I don't think it's working. The manual says to unlock the drivers door with the key, open the door but don't put the key in the ignition and after 20 seconds the alarm will go off. I do this and nothing happens. I set the alarm with the drivers window open and after a few minutes I wave my hands around the inside, shake the car and nothing happens. Any ideas?
The factory stereo has been replaced, could this have something to do with it?

 

I have not heard that unlocking the door with the key and waiting will set the alarm off. I do know there is a switch that sets the alarm off if the car is at a certain angle. Not sure if it is a shock sensor though. Try sitting in the car and locking the doors with the remote. Then open the door and see if it goes off.

 

If I remember correctly the Audi alarm system does use the radio as a ground signal so if your Audi has aftermarket radio the alarm signal will not see the ground signal.