My jeep had a soft top that was converted to a hardtop by PO. Are you still supposed to have the rubber pieces (door surround seals) under the hard top? I noticed on Ebay they're listed as a soft top part. The hard top does appear to have an indent in that area also.

Click image for larger version.  Name: seal.jpg  Views: 260  Size: 34.8 KB  ID: 37125