Sitting water like that wouldn't usually stink as if it gets in there like that, it would continue to drain out old an bring in new, or it would fill up really full!
However if it drains out right after filling, that little bit left over can get bacteria in it, and that's likely what you smell. Here is what I would do: Go to an auto parts store and look for the stuff you spray into the air ducts to eliminate smell. It has some kind of mold killing stuff in it. With the windows up, spray it down into the door toward the bottom and use it liberally. Then let it air out before using the vehicle as that stuff can stink for a while.
Don't drill any holes as it's just asking for rust to start in those spots after a few months. Even if it's not from water, that spray should kill the smell as it even works for dead animals. The main use is to spray it in the cowl when running the fan on high, because all kinds of crap ends up in the cowl like mice and rotting leaves and gets into the ductwork. I think it will work fine for you.
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91 Caravan 3.0 151k
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