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... OMG, will that $h1t ever stop???

 

that coolant leak sounds like the flange, not sure if the 3.0 has one though. Have you replaced all of the plugs? That's where I would start, then do all new coil packs.

 

I am somewhat more convinced that the issue is with fuel delivery but I think you are right in that I should check/replace the plugs as a starting point.

 

Your misfiring is almost guarenteed to be the plugs or the coil packs.

But if your worried about the fuel delivery it probably wouldnt hurt to get a new fuel filter while your at it, esp if the car sat for awhile. Should only take about 30min to get on there. Its right infront of your rear wheel on the passenger side.