99 VW Passat check engine light

I have a '99 Passat 1.8 turbo that has around 52,000 miles. The check engine light came on recently when I started the car after sitting overnight. The car runs rough when it's cold but runs great once it warms up. I had the car hooked up to a scanner and it said misfire in cylinder 3. I have changed the plugs. I have switched the coils around and I have switched the injectors around and it keeps comming up as misfire in cylinder 3. Can anyone help?
Any advise would be appreciated.

Is it an early 99 or a late 99? AEB or ATW 1.8?

A misfire could be caused by what you have already looked in to, spark plug, ignition wire(s), coil, and injectors. Since you have done all of that, next thing would be to guess that there is a valve issue usually caused by carbon buildup in the engine. This may cause a particular cylinder to misfire. Try a bottle of a fuel additive called
Techron. It is made by Chevron. Use the concentrated formula usually in a black plastic bottle. It should clean things up. You may need 2 treatments, if so, you must do an engine oil change after the 2nd treatment.