I had the same problem with my 97 SW rear windows. I looked into replacing the tracks and it was time consuming and temporary given the bad design of the OEM and replacement felt rail parts involved. The best solution I have found, and I have been using this now for over one year with complete success, is to get a small piece of rubber matting material, cut a thin strip, and then wedge the strip into the upper outside slider rail. I used black rubber from a matt that was designed to line a tool box. If you cut the piece small enough it wll fit into the rail and no one will ever know it is there. The only downside is that this will not work if you intend to actually use the windows. I tried this approach with other materials and nothing would last, especially if it became wet. However, soft rubber is effective and lasts nomatter how wet, cold or hot it gets outside.
With respect to soft top upper windows, I recently replaced the felt rail in my S-3 without too much difficulty. This quickly resolved the extremely anoying rattling problem I was experiencing. If the D-90 upper windows are the same as the S-3, all that is required is that you locate the small phillips head screws in the bottom of the felt rail, remove them, and then carefully pry out the factory rail. Replace the rail with a new one from BP, etc. and you are set. By comparision to replacing the rear sliding windows it is a piece of cake.
Just my personal experiences but I hope this helps.