After lowering car problem

No way would the tracking make it that bad just from lowering it. I would definately suggest that you take it to a garage to wack it on a ramp and drive the car whilst somebody is underneath, if it makes a noise, you know its the dirveshaft.

I'm not sure about the A3 but on other cars the danger could be when the drive shaft came out the needle bearings could have become displaced (at the gearbox end). We had this once on a Peugeot IIRC.

Its more than likely your driveshaft is the tripodic type on the 04 A3, its called tripodic because it has 3 corners as such with ring bearings is only way I'd describe them, that sit on each corner & gives it the flexibility it needs, this pushes into a socket as such on the inner part of the shaft nearest to the box/engine.

So its possible when you slipped it out, maybe you've dislodged one of the ring/bearing ends & its loose inside the housing, I would get it up in the air & have a play to see if there is any serious play on the inner joint, if so then need to remove it & check the shaft end inner to see if anythings amiss.

TBH its self adjusting back & forth, thats the point of the inner socket imho so its got some movement if need be rather that a solid joint with bearings, good idea tbh.

But if you hadnt put it in the socket correctly, I'd believe it would be extremely noticeable just moving of, not just corners.

Did you remove the shaft also from the hub end as sometimes this isnt seated properly & hence issues, mate had this after a cowboy garage did his upgrade of suspension, was exactly that, shaft badly fitted on the spline hub end iirc.

Given your issues, I'd remove the whole thing & check for any damage to the bearing ends, when you do these jobs you're supposed to hang the shaft up somehow so there is no weight on the shaft itself & no warp when refitting, which as much as I find it hard to believe as they're hard/thick as hell, but they're fairly heavy so any stress on the joint ends could damage the bearings hence looseness & issues reported.