I saw your posting and I had the same problem with rust at the jack points of a 400E I bought. POR15 worked great.

You can see my description of how to get the lower rocker panel cover off at;
W124 exterior plastic panel removal.

I also had a problem with water in the trunk lid (on the sedan not wagon). In this case I could hear water in the trunk lid after rain when I opened the trunk. In the open position the water would drain out the top corners with the drain plug removed. I traced it to a small hole at one of the bends on the inside edge of the trunk lid (but not inside the seal). In my case I sealed it with black RTV. To find it I spent about an hour with duct tape and a garden hose localizing the leak.

Good luck
Paul