Vent window assembly to door, lower seal doesn't fit

[Billhilly]

Pic's say it all. Completely rebuilt vent windows. Precision seals. All went together well, and all original holes used. Three small screws in the door frame all installed. Inside looks pretty good, rolled up slightly at the front, but if it was any higher the rubber lip might not be long enough to sit on inner door frame. Outside is clearly a different story. It's like the entire wing window frame/rubber is 1/4" plus to low! Left side isn't as bad. Anyone had a similar experience? Any ideas guys?