If I understand this right, you are thinking that the added weight of the window glass and hardware will affect the door adjustment? It wont. I was wondering why you intend to paint the backsides first, then the face sides. Primer overspray can still get to the freshly painted ineer sections.
Are you painting a metallic? I ask this because you mentioned painting separate leads to an inconsistent color match. Shops paint cars when apart most of the time. The trick is to hang the panels in the manner that they are mounted on the car. Doors and fenders upright, hoods and decklids flat. Spray the paint in the same direction that you would as if the car were together. Paint all panels at approximately the same temperature and with the same batch of paint.
One other idea...Paint the backsides and let dry for a few days. Flip everything over and paint the face sides. THEN assemble the car and spray two more fogging coats . I've done it both ways. Good luck.