I purchased my 2003 Towncar from an elderly couple with 65000 miles on the odometer. It was/is really nice, but just needed a good detailing. A few weeks after I purchased the vehicle it rained really hard. The next day I noticed water dripping from underneath the rear passenger side area. I opened the back passenger door and found 2 inches of water in the floorboard. After doing researching on a popular Lincoln forum I found the problem and solution. The problem concerns the outside HVAC air intake gasket. The gasket deteriorates over time and begins to allow water to seep into and around the HVAC plenum. Then the water travels behind the carpet and runs to the back passenger floorboard area.

To fix the problem I opened the hood and removed the cowl vent screen/grill on the passenger side at the bottom of the windshield on the outside (2 plastic Philips screws), then I removed the cowl vent tray which sits below (7 bolts). Next, I scraped the old foam gasket off the bottom of the vent tray and applied Black RTV in place of the old foam gasket and reinstalled it. The hardest part is drying the car out. I had to take the passenger side front seat out and the bottom portion of the rear seat. I pulled the carpet back and dried it with a fan for 2 days. The easiest way to keep the carpet up off the floor to allow air flow to circulate underneath was to put empty gallon jugs (with the lids on) under the carpet. The carpet is heavy because the carpet, sound proofing, and rubber backing is all one piece.

The previous owners stated that they garaged the car during their ownership and that it had been in a storage facility for a few months while they tried to sell it. I believe they had experienced some sort of problem with the leak, but obviously never had it fixed. The reason I believe this is because the car had a strong air freshener smell in it when I drove it home. I first noticed it when I turned the heat on high. The first time we took the car on a long trip my wife and I got really sick. Both of us got bronchitis. I did not attribute it to the car the first time, but the second time we went on a long trip and we both got sick and I started thinking that it was attributed to the HVAC system in the car. The next long trip we took we used a travel diffuser and diffused essential oil the whole time we were in the car. That seemed to work well. Recently we spent a significant amount of time in the car, but did not diffuse the oils and now we are both dealing with sinus issues, which is why I joined this site and reported the problem.

I had noticed a musty smell for a while, but we do not drive the car for an extended amount of time except when we travel. A few days ago, after getting sick again, I searched the web for ways to remove odors from the HVAC system. Using this information I sprayed Lysol in the outside HVAC intake for 30 seconds and ran the AC on high for 10 minutes and then sprayed Lysol in the outside HVAC intake for another 30 seconds and let the heat run on high for 10 minutes. I will do this often now. I believe the AC evaporator needs to be removed and cleaned and/or replaced. This would require the dash to be dropped and the HVAC plenum removed. Obviously this would be costly due to the labor.

Update from Sep 19, 2016: Spraying Lysol in the air intake while the AC is on high works wonders. Spray the Lysol for 30 seconds (in the outside HVAC air intake) and then let the AC run on high with the windows down or the doors open for 10 minutes. Then switch to full heat, spray again, and let run another 10 minutes. I used the Crisp Linen version of Lysol and the car smelled great. Do this every month during AC usage.