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Check to see if your vehicle has this "defect". Might be one way water is getting in the door.
Anyway, in the photo to the left of my finger, there was a small area (maybe 1") where the rubber was not fully seated in the track along the chrome strip. This is at the top corner of the door. It was noticeably different on the door that has (had?) the issue than the doors that did not. Yesterday, I seated it properly to match the other doors. It rained last night and we got a heavy downpour this morning. I just checked it and "voila" no pouring of water at the bottom.
This wouldn't explain why water is getting trapped at the bottom of the door, but just maybe how it is getting in the door?
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UPDATE: Ugh! Today I ran the hose only in the space in the bottom chrome strip (See post #51 in this thread) and the water did get dammed in the door. I few observations, however. When I run the hose nozzle on low in just that area while the door is open water does come out both of the weep holes in the door AND the weep holes in the weatherstripping. I believe what is happening is the water coming from the weep holes in the weatherstripping is getting trapped. Not sure how to fix it. The chrome strip part is now at my dealership. Maybe this will prevent water from getting in?