The two holes in the door are for screws that go into the bracket on the glass-run guide-channel (Factory Assembly Manual, Sheet 1, Section 22). There was a lock clip that ran between the two screws, and with bend-up lock-tabs on the lock clip.
I just now looked at that page in the FAM - I took those lock clips off my Suburban during restoration. The lock clip was not painted - it was raw/galvanized, so it looked like it did not belong there. Oh well, another day, another tidbit learned - thanks you all for pursuing this question/discussion.
Regarding the two holes above the door in the cab. They were not plugged in any of my vehicles (two of which had original cab windlace and original cardboard roof panels (undisturbed, in other words).
I dimly recall someone posting here a factory assembly photo showing the cab being held/lifted/lowered/installed onto the frame by an overhead assembly-line jig/hanger that used those hole above both door openings. And, as Greg noted above, I dimly recall finding a GM illustration of those holes not being plugged - they were described as being part of air-flow in the cab? I will continue looking for that information/illustration.
