I just got through fixing all my trunk leaks the other day. It took a while but now it's 100% leak proof.
I had water leaking from both tails AND both trunk vents. I replaced the tail light gaskets with some weather stripping from Home Depot (Ford gaskets are discontinued and not available anywhere). It's almost identical in material, but it's much thicker. For the trunk vents, I played around with the metal tabs on the car and bent them in a tiny bit. This keeps the trunk vents more flush against the car not allowing water to slip through.
I ripped out all my carpeting, spare tire, jack, jumper cables, etc. I took the "drain plugs" out of the spare tire area and hosed down the inside of the trunk really good and wiped it all down to clean up the old dirt and everything from the leaks. I replaced the side carpet with some from a Mystique at the junkyard which was in mint condition. Mine was all rotted on the back side from the constant moisture. For the warped floor carpet, I hosed it down really good and cleaned off all the dirt and while it was still soaked, I put a couple chairs on it with tons of weight. It kept the board completely flat and once it dried, no warp and looked brand new again.
Don't let the trunk leak for a long time. It can cause rust all over the place. And keep in mind when it leaks in the trunk, most of it will flow down towards the rear seat going right under the bench and getting trapped.
