Here's information on how to adjust a hard top. It might help reduce noise:
I'd advise you adjust the Hardtop, as no matter how hard the Germans or Finns tried, all cars will have flexed and 'settled' differently. If you have no leaks past the window seals when the soft top is up, use this as your datum and don't touch the windows at all.
a) Take off the plastic covers from each side of the hardtop and loosen the five alen bolts each side so you can just move the spinlocks in both planes.
b ) Open both doors and fully lower the windows, get your assistant to offer up the hardtop, clip in at the screen, make sure the spinlocks drop in, latch the top at the screen then make sure the top is sitting squarely on the car.
c) Give each spinlock a 45° turn, then carefully using a 5mm drill as a spacer, have your assistant gently press down on the top to provide a 5mm gap between the metal of the top and the bodywork on both sides, tightening the alen bolts each side. The remaining 45° turn on the spinlocks will make the top 'snug'.
d) Now have a look at the side window seals. On one side, gently pull the seal out of the aluminium channel - revealing the channel retaining screws. Loosen the screws enough to give some lateral movement of the channel. You will notice there is still a small strip of rubber on the outside of the channel - this forms the seal to the window. Now close the door and close the window, taking care that you and your assistant guide it into the slot with the small strip of rubber providing even pressure to the window. It doesn't require much, just even.
e) Hold the channel in this position, reopen the window and tighten the screws, then start at one end of the rubber seal and push back into the alumium channel in small increments. Repeat for the other side window and your hardtop will be fitting and sealing perfectly.
Here's the original post on Renntech:
http://www.renntech.org/forums/index.php?showtopic=10070&hl=hard+top