We also just switched from a regular Vanagon (over 30 years of various models) to an 88 Westy.  Yes, I keep asking the same question about wind noise.  We just returned today from a trip to Tucson and it was especially noisy when we were in very windy areas of the trip.  The previous owner had put a new seal around the poptop, but it's still noisy.  At times, I could even see the canvas blowing somewhat inside when there was a lot of wind outside.  Don't know what we need to do, but evidently some work needs to be done on sealing up the outside more than it is.  On different passes and some desert areas of the trip, the wind was very extreme and it got pretty noisy inside.

Sharon and Bob Mendonca
88 Vanagon GL
88 Westy