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If the leaves dropped inside the cowl vent, then the vent may need to be removed to get all the leaves out that fell in. The Dealer may have a fine mesh screen kit that can be installed on the underside of the cowl vent slots to lesson the amount of stuff that falls in, if theres not one already there.
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Check to see if your car has a cabin air filter, if it does not then there may be previsions to install one. This would catch the debris before getting into the A/C evaporator coil.
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The stench is already in place, so at this point the A/C evaporator coil will need to be disinfected and or cleaned to get rid of the smell.
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Consult with the dealer first before doing anything to get there recommendations. See if they will do something to fix this problem under warranty. Its worth a shot.