I had the same problem with the pasenger side. I opened the door one day, and there was a half inch of water on the carpet. Soaked that up and pulled the carpet up and there was another 3/4 inch of water sitting on the floor. Luckily my neighbor up the road had the same problem and fixed it. I did the same fix that he did and No leaks yet.
Pop the hood and look in the corner where the fender meets the firewall.
On the driver side the seam runs right by a Data plate that if I remember correctly had the VIN on it. I RTV'd the crap out of the corner where the seam is on both the Passenger side and Driver side.

 

it could be, but the thing is that on the drivers side theres also the opening where the air flows into the vehicle, so the rain will also fall inside there , i think that the best idea is to remove the wiper motor and transmission and use some of the stuff we use on floors when repaired , in my country we call it fendix, i believe you call it herculiner or something like that you mix it with some thinner and use a paint brush to spread it and remember that on the side panel there is a whole where the water drains , do not seal it , thats what i did to mine on both sides and there was no more leaks...

 

How were you able to remove the inside fuse box?

 

i did not remove it , i just put the tape where the fuse box and the firewall meet all around , its a special tape that looks most like bedliner but on a tape roll ...

 

My previous post was wrong. Sorry I forgot to update this. My jeep has been dry for months now, and in the Pacific Northwest that's saying a lot. As it turned out, the gasket that seals where the heater fan pokes through the firewall was leaking. Its a big job to remove, so instead I rtv'd the lower seam, and it fixed the problem. I found it by peeling back the carpet and having someone pour water down the outside of the car in different places, while I watched from the inside to see when water came in.