What i had done when my car flooded was this:

The smell was horrid from the dirty water. So i poured clean water on the affected areas and then shopvac'd it back up. I did that until the water in the shop vac was clean. Then used basic car interior cleaners over the course of the next couple of days.

Baking soda absorbs smells. Actually paint stores have this product where you pop the lid and it absorbs the smells. I think its made by Back to Nature.

Also leave the windows open to ventilate it if at all possible.

Thats all i can come up with.

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Brian E
Attending Falls OPC
Menomonee Falls, WI