Procedure for A3 Timing using VAG-COM timing graph
Note: Timing can be set using basic settings, group 00, blocks 2 and 9 in VAG-COM and a graph in the Bentley manual.
Tools needed. Laptop computer with VAG-COM v. 303.1, or higher. Suitable cable to connect to car from laptop. Flashlight. 13mm box end wrench. 13mm carburetor/curved wrench or stubby box end wrench. Straight screwdriver w/ cabinet tip. Stubby straight screwdriver. 1/4 or 3/8 ratchet with 13mm and 10mm deepwell sockets. 17mm brake line wrench, but a 17mm open end wrench can be used, if necessary. Pliers. Lubricant in spray can (liquid wrench/WD 40/Triflow/etc.)
Allow 2 hours for your first time with this adventure. After doing it once, bet I can do in easily in an hour or less.
Car must be at operating temperature to set the timing!
Remove the top cover from the engine by prying off the 3 circular plastic caps, and removing the 3 nuts with a 10mm deepwell socket. Unclip black wire from back edge of cover. Set aside after putting nuts in holes of cover and snapping caps back on. This prevents loss of small parts.
Remove the air supply line between the MAF and the air inlet snorkle.
Half way down black timing cover near center is a plastic screw. Remove with stubby screwdriver. Can use either phillips or regular. Careful! Easy to drop into bottom pan.
For the following descriptions, visualize a clock face.
Look at timing cover. There are latch clips at 1:00-2:00 and 8:00 that must be loosened. At 11:00 is a plastic tab that secures to engine that just needs to be lifted and pulled back. Timing cover will now be loose. Do not remove yet.
Note that at 12:00 is a small hose in a clip. Gently lift the top of the clip and slide out hose. Disconnect this from the hard plastic tubing, and place out of the way. At 1:00 is a clip holding two fuel lines. Remove from clip. At 10:00, inboard from edge of cover, is a plastic clip holding 3 small hoses (red, blue, black). The clip assembly can be released from timing cover by inserting straight-tip screwdriver at top of clip, and releasing tab. Pull away from timing cover.
Now that everything is released from timing cover, pull upward and remove from engine bay. Set aside. Reconnect hose at 12:00 position.
While you are here, take the time to examine timing belt. Look for cracking, ragged edges, etc. If you think there is a problem with anything, get it checked!
Look at toothed timing belt gear that is directly behind injector pump assembly. Note holes in it. Feel into holes for bolts at the 10:00 and 5:00 positions. If bolts centered in holes, you lucked out! If not, put car in 5th gear, and slowly roll car until bolt heads centered in holes. Using 13mm deepwell on ratchet, loosen bolts until can be easily "wiggled" with fingers. Usually 1 full turn. Do not back out so far that bolts can contact gear when turning!
Look at the end of the injector pump where the fuel lines connect. Reach under fuel lines, and feel 13mm bolt head toward the engine side of pump assembly. Using 13mm curved wrench, loosen 1 turn and wiggle. Can use stubby 13mm wrench, but much harder to do. Other members have stated that a 13 mm socket on a universal swivel works well. Somewhat easier if you remove the wires connected to injector pump on this end. Just squeeze the 2 metal wire clips, and pull away. Do not pull on wires. Reconnect wires after loosening bolt, or your car will not start. EDIT: a flex head ratcheting wrench works great for this bolt!
Start engine. Connect line from car to laptop. Start VAG-COM 303.1. Select control modules. Select 01-engine. Allow program to establish communications with car. Select 08-measuring blocks. In top row of boxes, use up arrow to change selected measuring block to 02, then down arrow to scroll to 00. Select basic settings box in left lower corner of screen box. Select timing graph box in right lower corner of screen box. Timing graph should now be displayed.
Note current timing as graphed on timing graph. Under graph is description telling you exactly where your timing is set. To change timing, perform the following steps.
Look at the injector pump. When facing from driver's side, note bolt at the 10:00 position. Loosen 1 full turn and ensure it passes the "wiggle" test.
Gently rotate pump. To advance timing, rotate toward firewall. To retard timing, rotate toward grille/front of car. A slight nudge goes a long way. Lock down the 10:00 bolt, and check setting on timing graph. You may have to loosen bolt and rotate several times until you get the optimal setting. I set my timing centered between midpoint and top of chart, for advanced setting. Note: If second person available, they can guide you while you rotate pump, saving several trial and error rotations. Tighten the 10:00 bolt securely to prevent further pump rotation and loss of settings. You may now shut off your engine. Next time I do this, I am going to roll down the passenger side window, and place my laptop on a sturdy stand beside my car so I can see the screen while rotating pump.
If your pump will not rotate, there may be some corrosion holding it to mounting surfaces. Lightly spray rotation areas of pump with suitable lubricant. Don't forget the surface in the area of the bolt under fuel lines. A little bit goes a long way! Under no circumstances should you spray ANYTHING on the timing belt side! Allow a few minutes to penetrate. Pump should rotate easily now. Do this with the engine off to prevent aspiration of lubricant into engine.
Release any tension on fuel lines to prevent breakage of line. Loosen fuel lines at injector pump and fuel injectors with 17mm brake line wrench. 1/2 turn is sufficient. Can use open end wrench, but be careful! Tighten but do not get overly agressive to prevent breakage of nut or damage to injector. Just make sure no leakage.
Tighten bolt under injector pump, and the two in the holes in the toothed gear.
Using VAG-COM, scan for any error codes that may have been generated by running engine with MAF disconnected. Clear these.
Reassemble all components in the order removed. Disconnect hose at 12:00 position to give you room to work. Also, don't forget to reattach small hose in the 12:00 position.
Enjoy the new pep that your TDI has!
Uwe and the gang at Ross-Tech, thanks for the phenomenal timing graph in the new version of VAG-COM. This made the job almost TOO easy!
Seriously, advice please. 
(that's one heckuva necropost)