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If we are talking about the factory soft top, the sizes are the same regardless of the model. The issue is that the zipper changed sides halfway through the TJ's production run. Years 1997-02 and 2003-06 are incompatible with each other. An early-TJ canopy needs early-TJ windows and vice versa. All complete tops will fit all TJ's.
 

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All the factory windows are the same size. The zippers on the rear side windows changed. The back window zipper is the same.

Also note 97-02, 03-06 fabric colors and weights changed.
 
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