I had a problem with my 99 V6 SE, i took it to ford and they told me they would water test it for me for like $100, and i was like to hell with that, ill do it myself. i got in the trunk with a flash light and had a buddy pressure wash the back of my car (at a coin op place) and low and behold it wasn't the trunk at all, it was coming in from a poor seal in the window. i had the window re&re'd for about $100 cdn, and when the took the back window off a strip of about 4-5 inches of sealer was never in contact with the body of the car. just a thought.
the water was coming in though the hinge on the drivers side.
hope this helps!!