PITA job. I have never got it right. There is a bit of leeway where the door hinges mount on the cab. You can move the hinge back and forwards a bit to help with setting it in a certain spot, then once one hinge is tightened up move the other hinge to wherever is best. Sorta the same as setting the bonnet hinges.
I usually get the door as good as possible then shove a wooden shim or two between the door and guard. This sets the distance between them.
Good luck and any info from other members would be appreciated too.

When GMH welded the bodies together it was all done on Fischer body jigs built for specific (Imperial) body gaps. They had to change to European jigs for Commodore, even the welders had to be changed, as the Fischer body jig panel gaps were too wide in tolerance for Commodore. So they were pretty loose to begin with. With the W size Holden and Statesman (HQ-WB) it was easy for them to float around as the body was mounted on rubbers to the chassis and the radiator support which anchored the whole of the front panels was also, then the guards joined the body, so when they put them together they must have left the bolts through the body rubbers loose so it could all be set up right. They would have had to do it with painted front panels too as regardless of which assembly plant it was the front panels were either painted with the body in the body plant or painted at the assembly plant (Elizabeth VAP or Elizabeth bodies assembled at Dandenong, Pagewood or Mosman Park VAP's). So there must have been a soft tool process for it. I have seen the Engineering Change Notice for the modification to ute and van bodies to change the little plate in the rear corners of the tonneau floor to a bolt on arrangement rather than welded, and it was around body alignment on the chassis as sometimes the rubber would fall off the chassis and then it was hard to get it back in place again with that little panel welded in place.

It is a double edge thing though as most of us when restoring a car want to get the body setup on the chassis, get it rolling and painted nice underneath all ready to get painted so we'd normally have the body on the chassis all nice and then try and get panels to align. Over the years with repairs and panels fitted to other cars etc it can be very hard to do.