It is hard to tell with my old eyes but it looks as if your entire door might be a little low. Raising the door so that the belt line matches will help the bottom of the door match up better. Could you also drop the outer cowl panel just a little to help that all match up?
I am going through this same process now with a 47 panel. I found that when test fitting the doors, all hinge bolts need to be tight. I started out by just tightening 2 of the 3 or 4 present at each hinge end (upper hinges at pillar have 4 bolts on 47-48). I then found when the last bolts got cinched down things had shifted just a touch. Securing all bolts helped much more than I thought it would. I also found that I could get more movement on the door vertically by having all bolts loose, lifting up on door and then tighten all. At first I was only doing the ones on the door separate from the pillar bolts. Doing all bolts on all positions gave me the vertical travel I needed. I had the lower rear corner of my door sticking out also. The front was flush with the lower outside cowl panel. I brought the top of the door out some to be a smidge above flush and it brought the lower rear corner in some. After that did not fix it completely, I tried another door. It was worse. I gave up temporarily and moved to the rear barn doors.
That has been a learning experience. I have 3 left hand doors and all fit different. I settled on the one the truck was born with as it fit best. It needs more work than the others but fit counts too. I could not adjust that door to fit well to save my life. I am using different hinges as mine were worn out and I secured a good tight set. The manual says to bend the hinge to get it to fit. So that is what I did. I heated it until reddish with my torch and gave it a few raps with the sledge. Bingo. Fits like a glove. I tell this story as it shapes my thoughts on the front door. Originally I was thinking the same as you stated. Uh oh, I got the bottom of the pillar too far out when I put in the floor and toe boards. Now I am going to have to take a slice out of them to bring the pillar in and in turn the lower rear corner of the door. Well, now I am thinking of taking the lower hinge and putting a slight angle to it to help the rear corner come in. It should not change to position of the front of the door being flush. Not sure if it will work or not. I certainly am enjoying your posts and progress. I will be waiting anxiously for your resolution.
Last edited by Twin Jimmys; 04/07/2022 12:09 PM.