I have the same problem, and I think it might be around the seal of the deck lid istself. I added some extra stripping all along the trunk edges and it seems to be fine now, though I haven't been in a hard long rain for awhile now.
-Electric Frost
1998 Mercury Mystique GS
SVT side skirts, rear SVT bumper, SVT exhaust, K&N Cone Air intake, 17in ST200 rims
2005 Ford Mustang GT
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