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Peace
Hard to say if the thermostat swap created the wp leak. Assuming the thermostat issue is resolved, you need to find the location of the wp leak - on the wp seals or elsewhere?
Rust is cancer. There is no any amount of sanding down to remove-the-rust is going to help you get rid of it. Like all rust, you can "slow it down", however it will come back. Only resolution is to "cut it out" and replace that section.
Body trim mouldings need to be completely removed for you to deal with the rust. Im guessing to it (the rust) is also behind the door panel skin (ie. you'll need to address it from the inside also (meaning you'll need to remove the inner door panels to access the back-side of the panel. It's alot of work - do a search on all the forums here and the others with "rust repair" and you'll find plenty of member thread discussions and DIYs addressing how-to on rust removal.
Optionally, depending on how bad the rust is, one can replace the damaged doors from a pickn pull - may be cheaper option.
Is it worth it? That's a personal call depending on your attachment to the w202 - ( emotion vs. economics)
GL
Peace
Peace

Ive used a product called 'rust check rust converter' for small rust spots - works incredibly well (for my situations) (however, nothing of the large areas as you describe.)
Best thing to do in your situation and economics, imo, is to DIY sand down the rusted areas to bare metal, and follow protocol to treat the area with POR-15 or similar, good primer coat and then the correct MB paint match touch up aerosol spray. Let it cure correctly before even attempting to make it purdy and shiny with the plethora of finishing product choices.
There is plenty of accessible uyube vids on the DIY rust removal and sanding etc you can review during your cold snap in NY. Plenty of reading viewing material.



