Stinky Soggy Passenger Side Carpet

Hey guys,
After a big rain here in SoCal, I found out my truck has a leak. Reading through a few threads on here, it seems like I have cowl cover problem and will need to be taken care of before the approaching El Nino winter. The leak left the passenger side carpet soggy and caused an unpleasant odor. I took the all weather floor mat off to let it dry since it's back to nice and sunny here but that didn't do much. After two days of air drying I still get condensation under the mat and the odor is still not going away.

Any idea how to get the carpet completely dry and get rid of the odor? The smell is driving me off the wall!

Thanks!