So I'm pretty sure the carpet and whatever matting they put underneath is done. It got wet, I used a dryvac, and there was no issue. There was a slight smell, it started to go away after leaving the windows down.

It happened about a month and a half ago, and the smell got stronger all of a sudden.

I am thinking of just replacing the interior (floor), how much do you guys think that would cost?

Any tips?

For the smell, try to leave a tray of charcoal and baking soda. It will absorb the smell. About the trace of leak it could be the a/c drain house.

Or you can get one of these.
http://www.autogeek.net/odor-bomb-car-fogger.html

You can also rent a rug doctor to deep clean the carpet before using dakota odor bomb.

Run the A/C on dry days...baking soda/coffee grounds (unused) absorb odors.

Definitely check for leaks in A/C drain trays/hoses as well as for tears (heavily worn spots) in weatherstrips. Good luck, Kira