When we bought our XJ the previous owner hadnt been driving it much at all the last couple of years. And since weve lifted it and been drving it a bunch weve had to replace the quarter glass rubber. Absolutely pouring water in. Well this morning my son goes to leave for church and the driver front floorboard is full of water. My question is....Is there anything on the drivers side that is notorious for leaking or could I have actually lost my seal on my windshield? He said appeared to be coming from behind/above fuse box area. Being its my weekend to work I havent had a chance to investigate.

 

Rust caused the same thing behind my 89 windshield seal.
The horn and wiper relays were ruined and so was the floor.
The windshield had to be replaced on mine to fix it.

If you remove your wiper arms and the grill cover along the windshield and possibly pull off the metal windshield trim you may be able to seal it with caulking.