All the links and issues I have found with leaking doors, missing plugs and tops in general are all in here.
Read the Where is my top leaking.
It will link to a sagging door, and replacing foam.
One of hte biggest issues that I see or hear of are the top frame seals that aren't positioned correctly to the windows.
They have a adjustment that if improperly set can cause the glass to not roll in to the seal.
See my how to install a top as it has tons of pictures as well.
where is my top leaking:
viewtopic.php?f=41&t=2655
another drippy knee fix
viewtopic.php?f=41&t=2737
does your "a" pillar seal meet the door correctly.
viewtopic.php?f=41&t=2690
If your "a" pillar seal is shrunk, it is acting like a rain gutter allowing water in to the vent seal.
You have to extend it so that it goes over the vent.
Your top should fit like flat.
A shrunken gasket.
How I repaired it:
Clean the edge of your "A" pillar seal with Alcohol and a rag, or Brake-Kleen on a rag get it clean You may need to use a steel wool pad to get all the dead rubber off. You have to get a clean surface.
Cover the vent wing with Painters tape. Get the inside to the outside.
Close the door
Apply Black Ultra RTV (it is about the same color as the seal Not in the picture). Do it so that you have a tapered edge on the seal to
Over the door, if you get it on the door edge no biggie as you want a over hang. I built it up over a few days to get a good strong bead.
Allow it to set and fully cure, about a day and a half.
When you are ready to open the door using a sharp x-acto cut the new rubber a little long on the door frame to separate it.
After the door is opened Remove the tape and reclose the door. You can then trim it to look pretty but still have the edge over your finger seal.
These photos are a re-creation for you.... I have already had to do this repair.
It was after my door was straightened to the frame and I had a good seal on the window to the top.