I had a similar problem when i went wheelin and ended up with water up to the door handles
my xj was totally swamped with water and mud it was not a pretty site
after taking 50 gallons of water out of it with my 8gal wet vac i let it dry for a few days until the mud harden then used carpet cleaner i think it was "409" to clean carpet.
it took about three weeks before all the smell was gone.
any carpet cleaner should do the job just make sure all the water is out or your jeep will smell like mildew all the time
Might i added my jeep still runs strong gotta love em