I just replaced the entire vent window assembly purchaed from classic parts. There is a pretty good sized gap between the seal and the door. No way it is going to seal anything. Is there a better seal out there i can use? Pretty expensive units to have to continue to throw money at but it is my daily driver and i would rather not have an aquarium in my door when it rains. My old ones were shot and the fit wasnt that much better.
I bought the weather stripping as the less expensive option and there is still an area that would allow water in. Not sure it's the same as yours but my fix was to run a clean bead of black caulk on the outside to seal it. The gap was very minimal though.
I ended up wedging some 4mm windshield washer tubing along the inside edge and it actually looks pretty good. This pushed the vent window unit out towards the outside. The remaining (outside) gap was filled in with sealant.
