My cousins took out the seats and lifted up the carpet. They sent me the pictures below. They were inspecting the floor pan to see if it would need to patched.

The floor pans in the front will need to be replaced or patched. In the back, only a small patch will be necessary. Like the 60's Mustangs, the Cougar was lined with with a cardboard like pad under the carpet, and it seems to have just absorbed all moisture, and caused the rot in the pan. 

Take a look at that carpet! It's 3 different colors. I see some coins in the pictures, maybe there's some gold bars in there too.