Bryan, It sounds like you may have tweeked the cab when you tightened it down. That is if the doors lined up prior to bolting down the cab.

You might check to see if you have the mounting blocks in the right place. If memory serves me there two different thickness blocks and the spring mounted bolts at the rear mounting point. Check to make sure these are installed correctly.

If your doors need adjustments, there is a way to tweek the door hinges to align the doors. These doors are not like the AD trucks. You can't make any adjustments of the doors by moving the hinge mounting locations. (You don't want to remove your hinges if you can possibly avoid it. A big PITA)

If you need info on adjusting your doors drop me an email. I've got a few pages from a 46 GMC manual that gives you the process that I can send you. The chevy manual doesn't have this section.

Good Luck
George