In this case, my preference is to leave the outer skin intact, but sand the edges of the skin where needed to release it from the inner, then you can cut out the old inner and replace it, using the outer skin to verify proper contour alignment before welding. Then replace outer skin as needed. If the door matches up nicely prior to removal from the truck, you can measure up from the bottom of the door skin (before the step I mentioned above) and mark a reference line. Then when installing the new skin you can again measure to this reference line to position the bottom edge. This would work well if doing this on a bench. If your gaps are not where you'd like them/need some work for better consistency, then I'd suggest leaving the door on the truck for outer skin fitment, so you can align to adjacent panels. In this instance, be sure to locate the panel for consistent gaps before making your final trimming.
