I'm not sure how good the gaps were off the assembly line, but as Carl 52 mentioned, get the rear gap at the belt line perfect. I'd next weld the new floor panel in and tack it to the new rocker. The front pillar and rocker panel should come together and fit provided the top to bottom length of the door pillar is correct. You'll have to raise the cab as it sagged in that corner. (I'm sure as it rusted but mainly when you you cut it out. The door will come on and off quite a few times depending on your tolerance straight gaps. You can use the replacement outer cowl panel as guide when you mock it up prior to welding completely. To answer your original question I removed the striker while aligning the door. I also welded my hinges in place once i was happy with their location. I made a world of difference with how the doors closed. I slotted the bolt holes (hinge to body) and welded off the side of the bolt hole and ground it smooth. Then ran the bolts in so it looks factory.
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