The gaps around the edges are adjusted with the shims, but the gap between the door and the weatherstrip is adjusted by angling the top and/or bottom hinges in and out.
General technique that works is to get the exterior gaps set first and then adjust the gap between the door(s) and body. For the former start at the rear, since quarterpanel is the only fixed body part while everything else can be shimmed (including the front fender and hood). For the gap around the weatherstrip use a piece of paper and feel for openings, you can use something like talcum powder to check for seal.
Note that the welded hinges on the body have holes in them which you can reach through to loosen and tighten the hardware for adjustment. The fender has to be off to do this for the front door.
