Update:

I have been quit on my progress, but concerning the door, I have continued.

I removed the inner corner again.

I seperated the step from the hinge pillar and took a porta power, between the rear right side cab mount and the hinge piller. With the door mounted. I then moved the piller until it meet the line of the door. Moved about 1/4 inch, but it looked perfect. I have not welded it in place yet, my plan is to put the cab on the chassis mount up the fenders and ensure the fenders line up with the door.