One area to check is the rubber conduit accordion which connects the doors to the front A-pillar, and the rear B-pillar.
The rubber accordion is a press-fit to the door and body pillar areas, and can allow water to run inside the pillars (and down behind the plastic trim panels and into the carpet and pad. Ensure it is firmly seated in the openings. You could remove the plastic trim panels and see if there are water stains from the area.
Also check the inside bottom of the all doors, to see if the drain opening are clear. If not, use the non-clasp end of a sturdy plastic zip-tie to clear the openings. If you use metal tools, you may scratch the paint which would encourage rusting due to the moisture and location.
It the door drains are clogged, or partially clogged, it can cause water to partially fill up the inside of the door, then overflow the bottom of the inside door panel (and into the carpet). If they are partially clogged, they can overflow - then slowly drain overtime and give the appearance that the drains are functional.
