I’m a newbie on site so please be patient with me. Recent purchase. I think the driver’s side fender and door may not be original. Any suggestions? Is this a common problem? Thanks.

Yes it can be. It could be the windshield seal or the heater box cowl seal also. You should be mindful of the junction box in the door pillar near your feet. Make sure it stays dry or it will get corroded and cause problems you can't find easily. Power for everything in the cabin goes thru that JB.

Hope these can help.

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https://www.cherokeeforum.com/f2/wet...-board-255393/
https://www.cherokeeforum.com/f2/water-cabin-249917/
https://www.cherokeeforum.com/f2/wat...-board-256047/