I have the same issue on the 2000 version, it has one Coil Pack on the front of the engine unlike earlier models with an ignition on coil system or four seperate "packs". I replaced the coil pack and it is starts a little better but still has a misfire issue??? I dont know where to go from here?

That is def weird, if you wouldn't have stated "due to fuel level" I would've ventured to say plugs/wires/coil. I can't even begin to think of what a fuel level would have to do with a misfire...besides the spark igniting the fuel, bad fuel?? I dunno but when you find out, please let us know.

Like Tonebone, I had the same problem in my 2011 Jetta SE (31k miles). Under warranty, took back to VW. They changed the injector, no change. Cleaned the valves, no change, did some other cleaning. Now VW has authorized them to put in a new cylinder head.

I hope this solves the cylinder 2 misfire low fuel code. I'll keep you posted.

2003 volkwagen jetta 2.0 cylinder 1 & 2 miss fire
 

Ok so for the past month my car has been giving me problems. A couple weeks ago I go to leave the house and my car starts idling weird and doesn't have any power over about 2500rpms. I drag it back to the garage replace the fuel filter and runs like a dream. Well a couple days ago I decide to go into town and it starts idling weird again and has no power so I drive it home about 5 miles away put it in the garage and brings up codes for a multiple cylinder miss fire, cylinder 1 & 2 miss fire. Oh yeah and it's had a p0420 for 02 censor for about a year now. So before I start replacing a bunch of unnecessary stuff anyone have any ideas of what it could be and how to test for it?

I'm having similar problems with my car so if you have found a solution that would help

2003 volkwagen jetta 2.0 cylinder 1 & 2 miss fire
 

Ok so this evening after letting all the snow melt off the car it runs without misfiring much at all. I'm thinking water is shorting it out somewhere. I'm gonna try new plugs and wires and see where that goes