Ahhhh, no the door opening didn't change shape. Not all trucks got the squared off roof. Crew cabs, extended cabs ketp the same roof.
You can swap doors between the cabs, just need the fenders so the body Ines match up.

So I think it's time to pop a door panel and have a look at adjustment for the glass, specifically if there is an up stop.

This is on just one side correct?