the rocker needs to go in so the fender gap to rocker is correct
you need the door installed & fitting the cab perfectly first to get the proper gap from bottem of door to top of rocker & so the in & out positioning is right
allso i use weld through primer on all inside areas of the cab & rocker so when your done you dont have bare welded steel trapped inside were you might not be able to get a corrosion ressisance coating the key to long lasting repair is to seal the metal on all sides from air water etc..

just sand it a little more
47 1st series pu 4x4