you're right, the 01 had the wind noise concern, the 04 had the transmission concern.
If your only problem with the car is that the gaskets scum up your glass, I'd be pleased. Just keep the gaskets and the windows clean. Go on the MBworld forums and see what some of their problems are, even on the all new S550.
My dad's 04 has like 70k miles, chrome trim is perfect. His 98 had 160k...chrome trim was perfect. My ES has almost 90k...chrome trim is perfect. Don't know what to tell you.
Just came out of an 07 CLS 550 which I had for 6 months nothing but problems....