I would have the water ducts checked specially the ones that come down from the sunroof, i would also check underneath the car to see if you have any holes down there some of these cars tend to have this problem but most likely is the water ducts
I had the same problem with my 2000 towncar, first check around rear window, next check below rear bumper, pop trunk , take a container of water and pour over rear window and follow the water around trunk channel and underneath car checking for rust spots etc,if everything looks good up top, lay beneath rear of car, you'll need a flashlight and maybe a marker of sometype to mark spots you find, first inspect side where water is coming in, following the water to all the nooks and crannies, now look at the other side and compare the condition of the joints where you followed the water on the first side, this will tell you what needs sealing, whatever the water touches that's where you want to seal,you can use silicone, or sometime of sealer, etc. you would never suspect this area because it's not in plain veiw.But anyway, Floor dried up completely, you'll have to pull up back seat and some door trim at floor to pull carpet back to air dry,or you could even use a blow dryer, you can also pull rubber drain plug in floor to help dry faster , then replace plug ,maybe use a disenfect to wipe floor before laying the carpet back out. If you never removed back seat, just pull forward and up,it'll come right off. good luck. this will do it.