If there's no more adjustment to move the whole door shell IN at the hinge area (you can use factory shims to move it OUT) then one solution is to shave down the surface of the hinge at its face, where it joins the door frame. You can take several mm off both top and bottom hinge faces. This moves the door shell IN towards the body, allowing you to use the factory shims to move it OUT to where it lines up. The wild card here is the front wing/fender. Replacements (new or used) are often subtly different in shape, and even originals can change shape quite a lot when worked on. Lining your door shell up to that can be a challenge...
It might be helpful to differentiate between the door shell and the (stainless) door window frame. Ideally you'd want to be lining up and gapping the door shell on the body first, and then fit the window frame and window. The window frame should be adjusted to fit the door shell and the rest of the bodyshell (door shell takes priority). You should be able to make it fit, as there is quite a lot of adjustment available in the various fixings. The window itself should follow the frame, but the window too has a lot of adjustment available via the winder mechanism and guides. It's a faff, but as long as everything is 'correct' (rather than Frankensteined together from unknown bits) it should be possible to get it lined up fairly well.
Door rubbers give endless problems. For me, there's no real substitute for the two-piece factory originals on a pre-73 car. The seals from Precision had a poor reputation for some time, and I believe they modified the design later? One of the problems is that aftermarket suppliers tend to supply a one-type-fits-all item when there was quite a big variation over the 9 year life of the S30-series models.