Some of the sub-pages under Interior/Door Panels above have animations of the interior of the Bug door. There is also an animation of how to remove the trim grommets without destroying anything.
Since I first did these repairs, I have found that Tyvek HomeWrap and Tyvek Construction tape are a quick and very effective repair for leaking vapor barriers. I'll have photos of that repair in the Golf doors soon!
The problem: water runs in when it rains. Maybe you replaced the door seals, or you otherwise confirmed that the water is coming from inside the door. It runs in from around the bottom of the interior door trim panel.