I just bought a Mk2 16v and mine had the same problem.
I took out the ISV and used WD-40 (I know what carb cleaner does to things, I work at a shop that uses it every day and its eats stuff alive) then took a air compressor too it. Then I added fuel injector cleaner and 93 non ethanol fuel too it. It runs so smooth now. Most of my ideling problems have gone away but there are some little hicups every now and again.
Ive been told to reground the cold start injector with 24g wire i believe it was to the engine? Who knows. You can go back to my introduction topic and read down where he tells me what too do. Also check your injector seals.
Other then that, im new to the whole VW thing so good luck man, sorry if none of this helped.