There are a couple of places that the HVAC system can leak and water will accumulate in the rear foot well.
One is where the HVAC drains condensate water. There is no tube. You can find the drain by removing the inner fender liner. A seal there deteriorates. It is more like a flashing than a gasket. I saw some pictures of it and a fix at www.crownvic.net.
The other place is the seal between the air intake screen (under the slotted cowel that runs the length of the windshield under the windshield) and the HVAC plenum. Water runs in there and into the front footwell, but it collects in the rear, I think there was a TSB issued for that.