Don't worry about it, honold. Yes, Mk4's are known for problems with window regulators, ignition coils, MAF's, and DV's (1.8T). But the good news is that the MAF's have gone down in price significantly and everything is under warranty for 4 years -- and even longer, because these are known problems. You could have bought a Japanese car if you wanted reliability, but you bought a VW because you wanted a car with character and style.
German cars in general have more reliability problems than Japanese cars; it's the nature of the beast. I could tell you countless stories about unreliable BMW and Mercedes from friends and family, and so could others on the net... Japanese cars have always been the resale value kings; VW never has been. Their reliability was always rated below average, but the resale value of the Mk4 has been higher than expected due to the tremendous demand for them. These were hot cars. Everybody wanted one. Now that the demand has died down, so has the resale value.
Don't fall into the trap of cognitive dissonance and buyer's remorse, scouring the net for all the reasons why you should have bought something else. Yes, it is a vocal minority; most people who have Mk4's that run beautifully are not going to waste their time on the Vortex. They are going to be out driving.
FWIW, my Mk4 has been going strong since I bought it in Aug 2001 despite using the driver's power window every day for security card access to my garage and dicking around with the air intake system, MAF housing, suspension, engine computer, door panels (I removed them and applied Dynamat to quiet the ride), and stereo system... (knock on wood)
It is a damn good car and you will love it. All cars have problems; some will have more than others. But basically, if you're lucky, you'll have no problems. If you're not, you'll get a lemon and be screwed. That goes with all cars, regardless of make.