the problem with the towncars is the cowel drains get plugged with tree debris both on the left and right side, from the cowel area not being cleaned out during regular services.
the drains get clogged and the water backs up and over flows into fresh air inlet for the blower case, it runs down the side and into passenger floor.
even though you are getting water in the rear of your vehicle breathless i would say the above is your problem because the floor of the town car is angled towards the back so the water is pooling there.
the drains need to be cleaned out and sometimes the cowel resealed. On the 98s the cowel drain under the wiper motor is the one that gets clogged the most, hard to get to without taking it all apart.
on the 03 and up town car there is a drain on the far passenger side, it has a little rubber door flap cover it. I cant remember if the 02 and previous town car has the same drain, i think it might.