The best way to describe building a truck is to start with the doors and build the rest of the truck around it.
You did the right thing by not welding everything solid. You may need to grind some welds where the hinge pillar meets the rocker panel and the floor so you can move the hinge pillar forward to get 1/8" gap front and back.
If you can't or don't want to do that, you can cheat by grinding the holes in the door hinges to allow you to move the front edge of the door proud of the outer cowl by 1/16" This will allow you to clear the door seal and have an 1/8th" gap at the rear. The Manual actually calls for "flush to 1/16th" proud of the outer cowl."

1952 5-window - return to "as built" condition | 1950 3100 with a 235 and a T-5 transmission