Removed the cowl screws and sealed the screws above the flap with black silicon, water stays out . parking the jeep nose down also helped.

 

The leaks are gone. Spraying the rubberized undercoating has stopped the leaking around the cowl. Sealing (seam sealer and rubberized undercoating) directly under the blower fan has stopped that leak.

 

when removing the dash first remove the left side harness held on by one screw, dash slips right over the steering column

 

Dealing with this now on my 89 XJ 2-door. It rains so much here in Vancouver that overnight the passenger foot-well will fill up completely and overflow out the bottom of the passenger door. Interesting thing is that it leaks if I park on level ground or facing downhill. If I park facing slightly uphill, I don't have any leaks at all so I don't think I'm having problems with the cowl snorkel. I've avoided this problem for several years by parking facing uphill.

By parking slightly downhill, a higher volume of rain is being collected on the roof and 'channelled' forward and down the windshield. I can't see any evidence of where the water is coming in - need to take another look at that antenna grommet.

As a side note: on one occasion last year when the foot-well was filled up for several days the passenger power seats stopped working. The 12V power pin in the seat power connector, which is 'live' all the time, was submerged and dissolved by electrolysis breaking the connection.

 

I would have a look at the blower fan as in my case it was leaking along with the cowl. There is a drain under the fan housing that can cause problems.

 

Mine turned out to be coming in at the top of the windshield. Fortunately my Jeep was going in to have some surface rust issues on the hood and roof dealt with by my body guy. Figured is there was something other then a remove, regunk, replace thing going on he could deal with it at the same time. Never know what the metal under there might look like till you look. Luckily for me it was fine so just a remove and replace.

 

I am having a leak issue on the passenger side of my 01 XJ that sounds exactly what you were discussing several years ago. I am in Richmond and could use some help.

 

I just purchased a 98 XJ, and had it delivered from long distance via car hauler in the rain.
after reading this post I went out and opened the passenger door, and felt the carpet......yup it's soaked!
There was many options mentioned about fixing this problem, and I'll post pics and results after I choose one, and pull the trigger on a fix....

 

I fixed my leak. The used a rubberized undercoating with a long nozzle (2ft). I sprayed, waited for it to dry. I used a flexible (endoscope) USB camera to look at the job and to cover areas I missed. Sprayed again. The other leak point I discovered is above the blower. This was a simple remove replace the gasket. No more leaks.