Need to check the fuel pump pressure, and then the injectors.
There is only electrical(spark, timing), air, or gas. Sounds like electrical has been covered, and air doesn't seem like it would be what you are seeing, so .... gas!
Oh, there are transistors that fire the coils, but when it happened to me on a different 1.8T, it was total, like one cylinder is totally not working. I think that's the normal failure mode. You'd know if you had this though; it's dramatic when you lose one cylinder on a 4 banger!