2001 Pontiac Bonneville Smell *Flood* please Help

I just bought a 2001 Ponntiac SLE Bonneville 71,000 miles. The thing is when I bought the car the Sun roof looked like it was kind of half in but it didnt seem to leak so I said alright its fine. Later on it began to rain and when I woke up the next morning the driver side and passanger side and the back seat floor and my trunk was soaked with water and it stunk bad. I then found out the sunroof tubes were not hooked up to each other so I got that fixed and then it all stopped but the Trunk and the drivers side floor is still wet. I cant figure out what it is and the smell has gone away in the front but the Trunk stinks no matter what I throw in there to keep the stink from going away. SO I was wondering if there is anything I can do to make the stink go away from the trunk?