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The new aftermarket drivers door was not exactly what you'd call a direct fit either.
A good way to fix the rust around where the window rubber sits is to take some sheet metal and form it to the shape, put some tar on the side that you wont see, drill some holes and pop rivet it to the truck. My truck had the same exact problem with rust there.
And when the rot you covered spreads that piece you put on there will fall off..Thats not a fix, but a temporary patch...