Congratulations on your success.
And good luck replacing the carpeting and padding… it’s a lot of work, but it goes quickly.
I should have specified. Straight hard top, no sun roof.
kolby12309 (http://community.cartalk.com/users/kolby12309)
February 26
Is there a sunroof? If so this sounds like a clogged drain.
The help is appreciated, but the problem is already fixed. 
Since AndyF is the original poster, wouldn’t they know if the problem is fixed or not? Unless I am misreading, I think you got confused by someone else posting a fix to their similar issue.
You can help yourself without resorting to expensive body shops but you’ll need some basic skills and tools. I suspect the leak is coming from the windshield or firewall area. Been there, done that.
First a few things- the carpet padding is not going to dry out by itself and there will be a serious mold issue if you do not act. Gallons of water will be retained by the carpet and pad. You need to get the carpet up off the floor and the pad removed to dry out. This will also facilitate you identifying the source of the leak.
Remove the sill plate along the door threshold.
Remove the lower kick panel by passenger feet.
If there is a hush panel underside of dash that is holding the top of the carpet, remove it.
Now you can lift the carpet to see just how much water is down there.
If taking the entire pad out is beyond your skills or desire, you can separate it along the connection points where it is dry and pull out just the wet section.
Wring it out and hang it to dry. It can be put back in when the problem is resolved.
Pull the carpet and pad away from the firewall.
Tape paper towels along the length of the firewall.
Close the door(s) and use a garden hose to flood the windshield, roof and valence area.
Periodically open the door and inspect the towels.
Water intrusion will be obvious on the towels where they get wet.
Look up from there…
Mental Notes:
These water leaks often leave subtle clues. it takes some patience and close-up observation to find the source. Another thing about leaks (either buildings or vehicles), is that the leak is sometimes remote from the puddle(s). It can run along wires and other materials and drip off away from the source or travel undetected under trim (carpet, etcetera).
Once I found the rain leak on my car I looked closely and could see tell-tale trails through dust, especially behind the door trim panel.
If I was going to try and track down an unknown source of a leak after no obvious evidence, I’d apply some dust, possibly from a spray (powder type deodorant or sneaker spray, etcetera). Then after a rain, take a close look for trials.
I actually found water droplets by close observation after a hard rain (and the fact I had an idea where to look).
Some leaks will come and go with the way a car is parked. My driveway has quite a slope near the garage. When the car was in the driveway nose-first the leak stopped, backed-in the leak started. The angle of the car can make a difference.
Carpet & Padding
I read my GM Pontiac Factory Service Manual about drying these materials in my car. GM differentiates between things like cotton containing padding and fully synthetic materials.
My manual said I had the latter (synthetic carpet and pad). Therefore it wasn’t necessary to remove anything. I removed floor mats and used a powerful wet-dry vacuum and got out as much liquid as possible. Then on a dry, hot summer day I left all 4 doors open and it dried completely. it’s been several years now and no smell, moisture, whatever.
CSA
Mold will grow on anything, including the plastic parts. Ask me how I know. It doesn’t matter if it’s synthetic material or not. Mold is everywhere. It’s just looking for the right environment to flourish. A consistently damp interior and a nice warm sun during the day…
I used an industrial carpet cleaner until the carpet was almost dry to the touch. Two days later, the car was showing signs of mold and mildew. Pulled up carpet and the padding was soaked. I wrung out GALLONS of water from that pad. The carpet had a rubberized backing…
You’re right. CSA’s post misled me.
@TwinTurbo
"Mold will grow on anything, including the plastic parts. Ask me how I know. It doesn’t matter if it’s synthetic material or not. Mold is everywhere. It’s just looking for the right environment to flourish. A consistently damp interior and a nice warm sun during the day…"
That is correct. Those microscopic spores are everywhere and travel anywhere! My BIL literally had mushrooms growing out of the carpeting in the back of a (relatively clean) car. It was quite astounding.
However, my proof in this case, is in the pudding. I read the manual, took a chance, and it worked. It’s been years and the only smell I have is that of leather seats when I get in my car. No mold, no odor. That puppy has stayed dry, even in our harsh weather above the 45th parallel. I do use rubber mats over the carpet to catch rain/snow on shoes/boots.
CSA
Here’s what I used and it worked great! I order factory manuals for ALL cars I have owned/will own. I can’t tell you how many times they have paid for themselves.
Factory Pontiac Bonneville Service Manual
“FLOOR CARPET DRYING”
"If the carpet or pad or insulator is wet, use the following criteria for drying or replacing the components:
-
For a 1-piece carpet assembly bonded to a cotton or a fiber padding, replace the entire assembly.
-
For a 2-piece carpet assembly with a cotton or a fiber padding, replace the padding only.
-
For a 1-piece carpet assembly bonded to a foam padding or attached to a synthetic padding, dry the carpet using the method described below.
-
For a 2-piece carpet assembly with a synthetic padding, dry the carpet using the method described below."
“Drying Method”
“1. If you observe puddles of liquid on the carpet face, use a wet vacuum to remove the excess moisture.”
“2. Blot the face of the carpet with a towel in order to absorb as much moisture as possible.”
"3. Point a fan at the affected area and air dry the carpet."
CSA
I’m a big believer in Factory Service Manuals as well. It took me a couple months to get around to ordering one for my last purchase, but now I can look up all kinds of facts and trivia. Even though they’re worth every penny, some folks cringe at spending say $40. But, it’s not lost money; you can use them to sweeten the deal when selling the car, or turn right around and sell them online once you’re done with them.
My latest ones were in the $150 to $200 range. I got a close-out price on the last set of Grand Prix manuals, $148.95 + tax + shipping = $171. Ouch! I cringed, alright. The “manual” is a 2-Volume set and weighs about 8 pounds!
CSA
Ouch is right! I found my two volume set on ebay for $40.
On those rare occasions when dad bought new vehicles, before he even read the owners manual, he’d go to the back page and tear out the FSM order card and mail it in. Moms been after me to do something with all those old manuals…
Never had a problem w/leaks on my Corolla, but I own an older Ford truck, and I’ve had quite a few leaks over the years. I think auto engineers have learned a thing or two about leak prevention over the years. I don’t see the year of your Lincoln, but if it is pre 1980, you’ll probably gonna have a few leaks now and then. You’ll just have to keep on top of them, so the floor don’t rust away and your Lincoln becomes a Fred Flintstone design 
.
The place you find the water puddling isn’t necessary where the leak is occurring. Suggest to get a friend to sit in the car while you spray it with a garden hose at full force from all directions. Spray from a step ladder down at the roof and along the rain gutters too. The friend may be able to spot some water dribbling down a wall or along a seam, etc. The leak in your case could be coming in from the trunk area, then moving to the rear seat area. Here’s the places I’ve had leaks on my Ford truck
- Fixed window moldings, at cracks due to sun exposure
- Window moldings for windows that go up and down, from distortion.
- Exterior rain gutters rusting and opening up enough to form a leak.
- Door moldings, due to distortion
- Weep holes in the bottom of door interior clogged.
- Leaves, pine needles clogging drainage system that is supposed to allow water hitting the windshield and going into the vents under the windshield. That water should drain out the bottom of a plastic tub like gadget onto the ground. When that pathway clogs, it causes the water to go into the passenger compartment instead. This is a major way for lots of rain water to get onto the floor when it happens.