I have leaking windows (driver/passenger), the passenger side has the biggest problem. When I park with rear end up hill it rain water drains into the car. Head up and it drains out of door when I open it. The fix is a new outer moulding/seal. The only place they seem to be available is Ford Dealers and they want $300.00 a piece! Seems surreal for a part that averages 35-45.00 on any other model. When I asked Lakeside Ford they said that was fair market pricing. All other dealers list same MRP. Huh? Anyone run into this issue or have a Mcyver fix. $600.00 seems a bit excessive to replace a couple of 38 inch pieces of rubber moulding. I've been looking for over a year.

 

Sometimes the door striker post can be adjusted to close the door tighter., providing that is how the water is getting in there.
There are drains in the bottom of the door to allow any water that gets in there to drain, outside the vehicle, check them..

 

The leak appears to be the exterior (outside) seal of window. Door drains, when I open it, so it fills up and has ruined the door speaker during rain. I'm just dumbfounded that such a simple OEM part is 300.00. Seems like a design flaw from which Ford is grossly profitering. Yeah, I know, nobody is actually shocked, eh.

 

Those seals cannot be 100 per cent effective because the channels the window slides in wears too.

Instead of attempting to fix what appears to be the problem, you need to look deeper into what is actually going on..

Those channels are adjustable and the door covering may need to come off to adjust for wear and the channels usually can be adjusted to get a tighter seal at the window's edge. You might consider having a good body shop take a look at the problem, they do this work every day..