Frequently the bottom of the vapor barriers become (or are left) unattached to the door when the window regulator is replaced. This allows the water that enters the door at the window to make its way across the door sill & onto the carpet. Get a roll of butyl caulk strip & use it to reattach the foam barrier to the metal door around the perimeter. Warming the door & caulk makes for better adhesion.
Vapor barrier is # 12:
Attachment 29627
Pic from ECSTuning:
Attachment 29628