sometimes it is hard to get the door to close fully if the door seals are toof irm from age and weather or they have been replaced recently and they are a little on the firm side. I have personally had this experience with a cheap brand that the owner installed and then brought to me with a tie down strap holding the door closed. I removed the seals, adjusted the doors to fit the opening without the seals and installed new softseal door seals and the door closed fine after.
first you gotta understand that the door needs to fit the door opening first and foremost. take the striker plate off the jamb so it is not pulling the door up, down, in, or out, then take the door hinge bolt covers off so you have access to the hinge bolts on the door. close the door and check the gaps and fitment at the top and rear edge of the door. this is where you need to adjust the hinges to get the door to fit the cab and not the fender, in fact I do this step with the fenders off so I don't try to cheat things. a wooden paint stir stick works pretty well to get the gaps about the same but you could go bigger or smaller if you want. if the seat is out you can get a helper in the cab, loosen the hinge bolts a bit, then the outside guy can shift the door a little to get a better fit and the inside guy can tighten the bolts after. just remember that a smaller door gap makes it easier for a bit of flex in the truck, going over a curb or a bump, can cause the panels to rub and remove paint. really tight gaps are for trailer queens not daily drivers especially if driving rural gravel roads (or you live in Calgary where the bumps in the paved roads are like driving a rural gravel road-minus the gravel. lol). once you get the door to fit the cab and close properly so it lines up with the body lines then you can install the door striker and adjust that so it closes the door but doesn't pull the door up or down. of course it is going to need to pull the door inward against the door seals but the seals shouldn't keep the door from coming to it's final losed position fully without slamming the door. also check the condition of the latch and striker to ensure it isn't worn out and allowing the play in the latch to let the door slip back open a little when it is closed.
with this done you can adjust the fender to fit the door. then adjust the hood to fit those panels. sometimes it takes some shimming inder the rad support or the front cab mounts to get the body lines to line up and not make the truck look like it is swaybacked. it is good to start with new cab and rad support mounts for this reason. another way to fine tune the body mounts is to hang a string line from the front of the front fender to the rear of the cab, along the body line but spaced just a tad off the sheet metal. then you can place some masking tape on the body line at the ends of each panel and mark the body line on the tape so you can see if the body lines line up to the string. I know, some of the panels have crisper lines than others so it is an average. when done take the string and tape off and see how it looks with a light behind the truck so you are looking down the truck panels and see a shiny reflection that will show shadow and details.
sometimes, if a door has been changed or a hinge has been swapped out, the hinges may need to be bent to swing the door so it isn't under stress when it is just hanging. once you get the gaps sorta good the hinges can be moved inwards or outwards on the pillar side to tighten the top or bottom of the door against the cab, then sometimes the gaps need to be tweaked again. I have some little wedges I use under the door to set heights sometimes as I work alone 99.9 percent of the time. a floor jack with a wooden block placed under the door has some merit as well. I have also used a ratchet strap, attached to the window opening and the airline on the cieling of my shop, to hang the door in an opened position so I can attach the hinges and not worry about scratching up the paint. some tape on the edges of the door, where it may rub other panels, is a given as well.
post up some pics as you go, it is interesting and helpful for others
here is a youtube showing a fella adjusting panels. he brings up a good point about the cab being square to the frame and how to do some small adjustments with the cab mounts to achieve a better fit
https://www.google.ca/url?sa=t&sourc...R7Gadzu9X5Mx9G
and another one from motortrend
https://www.motortrend.com/how-to/fitting-chevy-doors/
hope that helps and doesn't frustrate you. sometimes I just walk away for a bit when that happens.