Almost everyone suffers this same problem, and it's better or worse depending on which brand of gaskets you purchased. If it were the warmest part of summer I'd recommend leaving it out in the sun for several days with the doors latched to help form them into the correct set. If the truck is in a garage for the winter months a small heater set in the cab may help.
Make sure you have a small v shape gap where they join in the center bottom for the air to excape from inside the tubular portion of the gasket. This is even mentioned in the original Service Manual.
My doors fit perfectly before the gaskets were installed. After the gaskets, I did have to readjust them outboard a tad for several months, before I could reset them tighter again. With gaskets installed however, I never did get the doors as perfectly aligned as with no gaskets, and it's been ten years since I put mine in.
Here's a link that may be of interest depending on what you purchased:
http://67-72chevytrucks.com/vboard/showthread.php?t=363437
