I have the same problem on my 440 truck. Complete new weather strip kit, heater/firewall block off plate, full door panels and it has become air tight when closing the doors with glass up. 4 yrs old now still soft/tight. I have the habit of rolling the window down some as I get in.

FYI...It only took one time of my wife getting out of the stepside and closing the door not latching. Then the booty bump to close it put a big azz dent in the door. Then the fight started. I NOW Open & Close the door FOR her Getting In & Out of either of my trucks.

some time late 80s I think the doors got an air vent behind the lower door panel on driver doors. My JY replacement door on the stepside has the ugly hole with a plastic piece/rubber flap. I have short door panels and you see it. but worn seals and just about no weather strip on either door it is drafty so no airpockets when slaming doors.

have you tried open/closing the door a few 100,000 times to break in the seals?