I have had two Lincoln TCs, and both were awesome. Safest, most comfortable, and classic of any car I’ve experienced in sixty years of driving; however, each had a puzzling sunroof leak, surfacing only in the rear passenger’s side to the extent that puddles formed. Mechanics cleaned drain troughs but reported that no blockages, or leaking seals were present. A coincidence, or some shortcoming in design? I definitely won’t store my D41 in the backseat. So what’s the skinny?
check the bottom of the door. there are drain holes in it that can get clogged. water builds up in the door and can leak in from behind the door panel.
also see if the trunk is wet. it could be coming from their. if it is the seal around the trunk lid is leaking.
Any chance the sunroof seal could be hardened with age and not sealing?
It’s also unlikely that the sunroof was factory installed. These things were often done by an aftermarket installer. That may lead to a problem if you did not buy the car new and/or do not know who the manufacturer of the sunroof is.
Did they check the drain(s)?
Start by placing a small lawn sprinkler on top of the roof and getting inside, waiting long enough to see where the leak is occurring. That info should provide a good clue where you (or your mechanic) should be looking for the problem. It’s not possible to make a water tight seal and still be able to open and close the sunroof, so there has to be a mechanism, tubes etc., for any water that gets into the channel to drain to the ground.