Update:
A lot of the codes were something about "short to ground" so i checked the fuse box. The #29 Engine Timing 20A fuse keeps blowing.

Any ideas why?

 

Nevermind - fixed that. When he replaced the cats one of the o2 sensors was shoved up against the heat sheild, melting through the wire insulation and shorting out. Fixed that, we'll see if the codes are gone tomorrow, but I still seem to be betting some stuttering just below 2000rpms

 

Hey man, I'm having the exact same issue right now. The only difference is that my dash lights don't all flash, just the CEL. Then it will usually stay on.

I replaced the spark plugs 2 days ago and it fixed the problem for 1 day. The next day it started again. I did have some oil on the plugs, so I think my valve cover gaskets are shot, so I'm going to be replacing those ASAP. I think the oil was on the old plugs, replaced them so it ran ok for a little, and then the new plugs probably have oil on them again causing it to studder.

After that would be the coils, but I'm a little confused about these. When I look at the engine, this is in the middle-front:


but isn't that the ignition coil? Is that different from the "coil pack", which looks like this:


My car is a 2000, I hope we can figure this out without incurring too much cost

 

It depends on the engine. That first picture is the Ignition Control Module for the 2.8L engine. The second picture is a coil pack. The 1.8L engine has a coil pack on each spark plug. The first picture is bascially 6 of the second picture combined, with wires running to the spark plugs.

I just did the valve cover gasket - which was bad. It was an easy job, but I just noticed sparking between the spark plug wires - so I'm gonna do those tomorrow and see if that helps

 

I also replaced the valve cover gaskets, and like you said, wasn't difficult at all.

Now that I've been under the hood so much the past few weeks, I understand the coil pack/ignition control module difference.

I just had the CEL code pulled at it was a misfire in cylinder 3. Turns out it was the spark plug wires. Replaced them yesterday and it's good as new. The wires are expensive for our cars (~$160 for the OEM Bosch). Hopefully the wires fix the issue for you too. Let us know how it goes

 

Did you ever find out what was causing this. I have a 1.8t with dash lights flickering and a huge stutter. It really only happens when im boosting hard. I lent out my OBD II computer but autozone gave me P1300, then I have misfire codes for each cylinder also a code for MAF sensor. Replaced coils and MAF to no avail. I think its electrical because its been extremly wet for the past week. It also happened right when I put in a new turbo so it was probably an issue before, I just didnt have the boost to realize it.