but I also have this procedure on file that is similar:

Step 1) With one key, turn the ignition switch on. Don't start the car, just turn the ignition on so the instrument cluster lights up.
Step 2) Open the window. Not neccesary, just a safety precaution to keep from locking the keys in the car :-)
Step 3) Close the driver door and lock it with the other key.
Step 4) Hold down both the Lock and Unlock buttons on the remote for a few seconds (may be upt to five seconds). After a couple of seconds you should get the honk and flashing lights.
Step 5) Open the door with the key, and turn off the ignition.
Your remote should now work.

• http://www.audiworld.com/tech/misc13.shtml

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It's not quite stock:
Build date 02/01 | APR 93 | Blueflame Exhaust | tCarbon FMIC | SPEC Stage 2+ clutch
KW V1 Coilover Kit/K-MAC | DEFCON 2 Control Arm Bushings
Neuspeed 19mm Rear Sway Bar | DieselGeek Short Shifter (original)
Schwing TTDA Stainless, full front feeds | Schwing BAMM/MOFO - Stainless (w/4.0 FPR)
Boost Machine (my build) | Samco Intake hose
Powder Coated Intake Manifold | EvoShield Intake Gasket
ECS Slotted Rotors (Brembo/Zimmerman) | PBR Ulimate Ceramic pads
Stainless Brake Lines - front | TyrolSport Caliper Stiffening Kit
Dogbone Bushing (Energy Suspension) | Damplifier Sound Deadener
AutoMeter Boost Gauge w/APR Gauge Pod | Engine/Chassis grounding kit
SFS Performance Upper IC hoses | Greddy RS Diverter Valve (relocated)
Raffi Speed-2 Shift Knob | Valentine One (hardwired)
Euro Blindspot Side View Mirrors | Sears DieHard International 33347 battery
Smoked Side Markers | Window Tint (35%) | Tinted Euro Tails (amber blinkers)
Bosch Aerotwin Wipers | Riso Zero | Clear Corners (OSIR Design) | de-Spoiled
TT Valve Stem Caps | Alpine CDA-9820XM head unit (XM integrated) | Scangauge II
18" RS4 reps/Toyo T1r | Eibach spacers 15mm front; 25mm rear
42 Draft Designs 3" Downpipe | liquidTT gauge | 42DD Engine Cover Hardware