I did this job on my 74 240D 4 years ago with great results. I used 18 Gage soft steel body plate because it easy to form into the floor contours. All joints where the new meets the old good metal were pop riveted with steel rivets, not aluminium. Any rust left behind was killed with a product from an auto paint supplier. It turns the rust black and ready to paint. To water proof the in and out surfaces I chose not to use under body coat but instead, at the advice of a car restorer, I used a rain gutter sealer. The stuff is black, very sticky, long fibers and can be built up to a good thick and tough layer like what is on the bottom from the factory. It will dry hard in 3 days and can be applied to a wet surface. From Home Depot, get the trowel grade.
I had to replace all 4 foot wells.

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1984 300SD turbo 126
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