Two leak locations that have soaked my trunk over the years were:
1) Air exhaust vents. These are plastic inserts (mine had cracked) hidden behind the fender side trunk liners on each side. They snap in from the outside which means (at least on my SVT) that the rear bumper cover had to be removed to install the new vent.
2) Small leaves, maple seeds, misc. dirt builds up behind the tail light pods so that water drains into trunk instead instead of around the light and out. Easy fix. Pop out the module, clean, and you're back in business,
