Hi,
you could try to get the timing utilities for the belt from your local Audi dealer. Usually they have it and if they are nice, the give it to your for little or no money for a day or two. I would ask!
You are right, the teeth are important for the ECU. It is a very interesting fact that it still seems to work without troubles even though you lack some teeth. It is also true that a lot of people are so stupid that they use the flywheel to get the required force to open the crankshaft bolt in the front. That, by the way, caused a major breakdown to my 220V on my way back from Sweden some years ago (yes, I also was that stupid). You can buy the other part of the flywheel without having to buy the whole thing, as war as I know. I'd think about exchanging it, even though it still runs.
It is also common that the engine mounts wear out over time which first causes strange noises and vibrations and second causes troubles when working on the engine without removing the front. So that's probably a reason.
HTH
Bastian
