It is very difficult to align the doors with the weather strip installed. It is also very difficult to put the weather strip on the door while it is installed. A conundrum wrapped in an enigma.
It would be best to remove the door to put on the weather strip.
I am in the middle of this very process with my painter. We aligned the doors, then drilled holes through the inner door and hinge straps for alignment pins for easy realignment. I will get back to you on whether that works out as planned.
Carl

1952 5-window - return to "as built" condition | 1950 3100 with a 235 and a T-5 transmission