Looking at an earlier post of yours you state that you can see water on the top of the sills.
That is OK. It's when the door fills up and allows the water to flow out the door card/carrier plate over that sill into the car. If you sealed you door correctly, ideally with Butyl strip it should be good for a long time, just make sure the drain holes are kept clear as well.
Did you check the cable entry from the bulkhead? Have a good feel on the carpet behind the foot pedals for signs of damp.