Although not a solution, this sounds very simular to a problem I had with a mk2 GTI. Just tries to stall while driving at certain RPM and then it's fine again. I was always told it was fuel evaporation which was a common problem with old VW cars...
Have you tried something as simple as fuel line/injector cleaner, just to make sure the fuel is getting to the engine correctly? Also, when was the last full major service where the oil and spark plugs where changed?
