I originally posted this in the A4 B6 section but I am getting very little response...
After getting my 2005 A4 3.0 from the dealer lot where it sat since last August I already replaced the totally dead battery, a dead HID bulb, and the turn signal issue seems to have resolved itself.
Now the car was low on fuel (with the reserve light on) and while I was driving it to the pump it started shuddering and running rough at idle and low RPMs. After filling up I ran the vagcom and got several misc misfiring, on different cylinders. I cleared the CEL and drove it a bit more to see if the misfiring followed specific cylinders. Nope, different cylinder would misfire, according to the vagcom.
I figured the issue was related to old fuel in the tank (sitting for 7 months) and possibly a small fuel blockage. I got some Sea Foam and poured in the tank and tried running the car around the block a few times but the car still misfires. I realize that I may need to drive the car a bit more to get the full effect of the fuel/injector cleaner, but I am also concerned about driving the car with all the misfiring.
Would replacing the fuel filter help? The car only has 27k miles.
Should I keep driving the car or is the risk of damaging the cats too great?

Thank you for all advice.

In addition I also noticed that the car is leaking what seems to be coolant at the back of the engine, on the passenger side... Crap!!!