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 
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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.