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Check your spare tire area. You most likely need to replace the tail light seals. My sister's car had the same problem this past summer, although it wasn't bad enough to go to the rear floor, just filled the spare tire well. The dealer has new seals for about $15 each. Also a good idea to use silicon on the tail light retainers.
You should also gut the interior, IMO, to completely dry the insulation under the carpet out to prevent mold. Been there, done that. PITA but my car doesn't smell funny.