So after I fixed the holes in the floor, and got them watertight, it's been raining very hard here today so I decided to go ride for a bit, got it back home and started pulling edges of carpet back to check for any water, and in the rear cargo area on the passenger side there was a trail of water, looked like it was coming in around the seals on the 1/4" windows. So I started checking things out and I found 2 small holes, maybe 2mm long on the front and rear on the bottom of the gasket on the outside, The driver side has little notches but the passenger side where the water was had holes all the way through, I blew through them with my air compressor nozzle and I could feel air on the inside of the jeep in that area, So I just took a tiny gob of silicone and stuck it in the holes, maybe that will take care of the rear leak.

Driver side where the water was, there was a hole at the front also.



Passenger side. Dry as a bone on the passenger side.

 

Those look like they were factory weep holes. If they are, you shouldn't plug them as they are there to allow water and dirt to escape from under the moulding thus helping prevent rust.

They would be along the bottom edge of the moulding only. Water shouldn't be coming in there for sure.

Happy Jeepin'
TexasTaz38