I wanted to relate my history with this problem for both my own education and hopefully to be helpful to others.
About a year ago water started coming into the cabin during any significant rain just in front of the gas cap door lock (next to the threshold). I removed the inner lining and did the hose test. That water was coming in from both the speaker hole and from a small 1.5" hole above that. Drainage holes in the bottom of the door were wide open. So, I got some plastic and silicone rubber and sealed the small hole outright. To solve the speaker hole problem, I glued small sections of plastic (like from a plastic bag) in an overlapping fashion above the speaker so that the sections would lay over the back of the speaker and shed the water past it and on to the bottom of the door.
I also replaced the rubber window trim on the outside of the door to do a better job of sealing the rain out as the old was a little stiff. This helped but did not eliminate the leakage by itself.
My remaining question is why did it start leaking at all??