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.)
2003 TJ, 33" BFG AT, 2" BL, 2" BDS spring lift, Truck Lite headlights, Homemade sunrider top.
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?
I have the same problem on my 1997 Wrangler in exactly the same place. When I got it from the factory it was perfect. I think it happened when the dealership installed my light bar. I forget exactly what happened but I did get a new weather stripping while it was under warranty. The dealership said that they aligned the door, and right away it was torn again. The dealership sort of gave up. I have been dealing with this problem for 16 years!! My drivers door weatherstripping is all ripped up, in the top corner, and I don't want to keep replacing it, just to have it rip up again. My passenger door weather stripping is fine, so I don't imagine it could be my top. Otherwise, it would seem that both sides would be torn. I would love to solve this problem after 16 years. (I'll post pictures of mine this weekend.)