Passenger side leak on floorboard(not coolant)

So I've been having this leak on the passenger side floor which is water. I checked under the cowl and its relatively clean. I sprayed water on nice and easy with my hose and it poured out onto the ground so I assume that's not an issue. I checked the AC drain and its dripping water after use so I assume that's not it. The seal around the window looks like its in good condition. What else could it be? It's leaking from what looks like to be the heater/blower box? It has a flap on it that opens and closes with a vacuum actuator and when I push that open with my finger it seems wet inside there so I'm assuming the water is coming from inside that box. Again making me assume its the AC drain but that seems to be working? Anything else it could be that allows water to leak in that way?

Doesn't sound like it, but could it be one of the screws holding the roof rack rail?

If you take out one of the screws, you'll find the nutserts have a hole in the bottom that goes through to the interior roof area. If water is penetrating, it could potentially run down the A pillar onto the floor.

I had some pin holes under the carpet on the passengers side floorboards. The tires turning would force water through those holes when it rained.

The pinholes and minor rot can be hard to see. I use a wire wheel on an angle grinder and this will show up blistered paint and rust under the paint quick. The problem is those minor holes can turn into big holes and major work quick.

You can use the same wire wheel underneath, loose undercoating and blistered paint will show itself quick.

I use a paint over rust paint, Hammerite. The half flat black dries quick and bonds well.

It is a pain taking the seats out and lifting the carpet, but neglecting it can be a whole lot more work in the long run. I did close to 60 hours of welding and painting on my wifes 96 this last winter.

Can also be the antenna wire. It runs down the wire and through the grommet. Pull kick panel and seal it up with rtv.

This type of water leak seems to be a common problem on later model XJ's...here's what I did to fix it on my '98.

The first culprit I suspected was the plastic air intake that located under the windshield cowl. You have to remove your wipers, and remove the cowl cover. The intake is underneath some sheetmetal, that obviously prevents water from pouring straight in. I cut the sheet metal away just above the intake. Once I had a hole large enough for my hand to fit in, I simply applied some sealant around the plastic cowl intake, where the foam seal is to seal it off. I then used some plastic sheet to make a "patch" over the hole I cut in the sheet metal. Seal it up with silicon, and you'll be fine.

Unfortunately, this wasn't the cause of my leak, but it was good preventative maintenance since I figured the foam seal around the cowl intake won't hold up over time much longer.

This led me to then next possible area for leak, and that one being the foam seal where the blower pokes through the firewall on the passenger side. Pop your hood an take a look at where I mean.....that is an easier fix. You might have to move some piece of emmissions equipment that sort of blocks your access to the foam sealed area, but its only a couple of bolts, and you can lay it aside. Once you have clear access to the blower seal, just apply some silicon all around where the blower meets the fire wall to seal it up, and seal up the foam really well.

Also, there is a wire loom that runs along the fire wall above the blower, that splits off towards the fender, and then runs down towards the engine. In my case, water was dripping off that wire loom and dripping straight into the blower area. That was the source of my leak. Take a look at yours, I bet it's doing the same thing. Just zip tie that wire loom aside, so that it no longer overhangs above the blower.

I haven't had a leak since...

I think it's the fresh air vent. I sprayed water into the cowl and although 99% of it poured out underneath it seems as though inside the blower box it got wetter then what it was. I could not tell how or where it was coming in it just magically got wet. Also it's only when it rains a lot and its sitting. Like if it siesta over night and it rains ill come out and there will be a puddle.

Okay so I ran the AC yesterday a while when I was out and about in the 100 degree weather and it seems it leaks with just the AC running for a while? Wouldn't that mean the condenser drain plug is blocked? Bc I can see it dripping out from underneath still. And when I park it leaves a little puddle. Could it be partially blocked? It doesn't make any sense to me. Maybe I have two leaks?