There is a phrase which was coined (maybe by me) about the "Ring of Death" regarding the door opening. It is in reference to the "ring" which consists of the hinge pillar, latch pillar, rocker panel, and the top of the door opening. If any portion of this "ring" is broken and not restored to specs, your door won't fit. It sounds like you broke the Ring of Death at the rocker panel, but got it put back together pretty close, based on your current fore and aft measurements.
Does the beltline of the door match that of the cab, front and back?
Also, it will help the alignment procedure if you remove the striker at the latch pillar.
Carl