Thought I was done with this but only temporarily moved a blockage from over the drain hole, as I discovered as it rained all day today and I had another flood in the passenger footwell, soaking my O2 sensor connection and giving me crappy mileage and doggish performance. So here is what you need to do if you have this problem:

Use a hooked probe to go up into the drain, and pull the entire rubber stopper out. It is essentially a cone within a cone. The outer cone is a rubber funnel with a wide spout. The inner is a cone with three small holes in a triangular pattern. Small debris and sludge will easily clog them.

Use scissors to snip the rubber between each hole. You will then have a large triangular opening that water and small debris will easily flow through. Replace the stopper (I don’t know what else to call it) with the outer cone pointing back towards the rear of the car. Hopefully, that will do it. (And luckily, I have not yet replaced the lower carpet. After 7 days, is still not completely dry.)

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2008 E350 4matic / Black/Anthracite

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Gone but not Forgotten:
2001 E430 4matic, 206,xxx miles, Black/Charcoal
1995 E320, 252,xxx miles, Black/Grey
1989 260E, 223,00 miles, Black/Black