I hear you. I have a door that does the same and I have not found a solution otherthan maybe take the door off and reshaping the upper part of the door (which will definitely have implications to the window glass). As is your case, the gaps and alignment on my door is about right and any adjustment will throw things way off.
If you move the door your gaps and latch will not be right and I think that will bother you even more than the water (from time to time).
How much driving-in-the-rain do you do?
I keep the gutter on the roof free of water after a rain to reduce the chance of rust IVO the windshield, which is a prone area. This is where all that water comes from as is drains through your door.
The other side to consider - give that water an easy place to drain. Make sure the drains at the bottom of the door are open and maybe allow for the water that makes it to the floor a path to drain.
I cant provide a solution to your problem. I am in the same pool - so to speak.
