Bringing your thread back alive since I'm would like to add power windows into my 65 Dart wagon which is in the process of converting it into a 2 door sedan delivery using 66 doors sedan doors along with the the B pillar. I hope to avoid your alignment times since the window is only up and down.
I found that most of my alignment issues were my fault. I didnb't clock the motor enough to get the range of movement once I removed the motor and moved the motor position to the best position and it aligned fine.