That happened to me to. You may want to try moving your top back. It looks a little close to the door. I read that to readjust the hard top you can't simply pull it back. You have to lift it and reposistion. Worked for me.
03-06 tops have an alignment pin on the drivers side of the top. 97-02 do not. All tops are the same size and are interchangeable. I'd release the header latches, loosen the 6 bolts for the top and try to pull it back. There might be some play. If it is not that, your door is out of alignment. You are going to have to adjust the hinges. (note I wouls not have let it go this long, now you have to replace the weatherstrip.)
Is there any straight up and down movement in the door (can you lift it straight up)? To me, it doesn't look like it sagged, but it does look like it could possibly be a little higher (really hard to tell the clearances in the pics). Could be that the rings are worn off the bushings between the hinge leaves maybe?? How does it compare with your passenger door?
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