Oh man, I have a very similar problem with my 99 Passat 1.8T, please keep us informed! Heres my thread from the VW forum.

Hey!

My wife was driving the car and it all of a sudden started misfiring bad enough it was undrivable.

I will start by telling you the work I have done so far and I still haven't solved the problem. I did a valve cover gasket and plugs after I realized oil had seeped out of the grommets and all the way through the spark plug threads (it ran perfect for 2 miles and started misfiring again. I then did all 4 coil packs and plugs again because 3 of them were covered in carbon after only driving 5 miles most)

I am getting 2, 3 and 4 cylinder misfires on the diagnostic.

I did a search of the VW forum and found problems with some similarities. Old threads and no real answers (my situation is a little different anyhow)

I'm in this problem for about $500 and hope someone has had similar or suggestions.

The car still runs and the misfire is less once its past 2300RPM or so.

Any suggestions would be greatly appreciated!

-Jason

 

I kept having random misfires and though the car was still drivable, it was getting worse. I ended up taking it to the stealership and they said that they had to re-program the computer. Supposedly that's going to fix it.
I'll see what they say tomorrow when I pick it up.

 

WHAT? you bringing it to the Audi stealership? umm...be sure to bring,plenty of lube with you,my friend as they are planning to **** you over!

 

it was my ignition coil control unit

http://www.partsgeek.com/gbproducts/...ek+Google+Base

Goodluck if you have the same problem and be sure its not something else and don't let a dealership rip you 600 for this 140$ part!

this is the link to the 99 audi a4 quattro ignition module http://www.partsgeek.com/catalog/199...trol_unit.html

 

Well, I took it to the stealership. Those punks "re-formatted the computer" for $190. They asked me to change the spark-plugs for some stock that they had to sell me @ $50 (!!!). They wouldn't do anything to the car w/o changing the spark-plugs. They wanted to charge me for changing them, I told them I'd do it.
The car now runs smoothly!!!

 

Wow....so you got the "computer re-formatted" and new plugs and it runs ok now?

 

That's right. They said that the computer was messed up and the'd upgrade the firmware.
I had just changed the plugs for some nice ones, but they didn't like them.

 

Well I'm glad that it all worked out brotha! Where are you located at?

 

...UT

 

i had the same problem with misfires...multiple misfires...i changed the fuel injectors, fuel filter, spark plugs, coils, the ect sensor...none of that work...so i brought it to this one audi machanic and right away he knew what was the problem...for mines the cam was off timing and it caused all those problems...placed it back in time and now its back to normal...so maybe check on your timing.