So an update on the leaking issue.....
Friday it rained from around noon through the night (we got about two inches). I waited until about 6pm on friday to check for any leaks and opened the driver side door to find that all was dry. Now upon opening the some water drips in. I shut the door and went in for the night.
I went out on Saturday morning and found about an 1/8th of that "tray" below the door had water in it. When say an 1/8th....so the car sits in my driveway which is uphill. So the water would tend to pool toward the back of that tray. Well pooling toward the back of the tray the water didn't if come up to halfway to the top of the tray. That creates questions for me.
First the positive, even if it's still leaking a little bit it is way less that it did before (meaning that tray would have been full before).
Now the questions it caused.... so I know that between noon and 6pm (when I didn't touch the doors at all) it was completely dry. Then I open the door and some water leaks in. Now, the reason I had some water in that tray on Saturday morning might only be because I didn't shut the door right (correctly insuring the window sealed) after I checked it at 6pm on Friday (which might have caused a small leak) or that water could just be what leaked in when I opened the door to check it as well. Either way, I think I'm pretty close to fully stopping the leaking (at least on the Driver's side). *Knocks on wood to not jinx it.