How do you adjust the vent window frame

Looking at this again, its seems your top is out of alignment, not the glass. Look at update pic #5 and compare that to update pic #6.
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That's what I was thinking too, especially if the top has been replaced.

Is the bottom of the door parallel with the top of the rocker panel? With rebuilt hinges I would start there and adjust as needed.

You probably know the striker pin is adjustable as it threads into a floating nut held inside a cage on the back of the B pillar. You do NOT want the weight of the door resting on the striker pin while driving. The flanged bearing surface of the pin is only the single thickness of the B pillar. Maybe18ga. Over time the sheet metal fatigues and breaks, with the door usually jammed closed. I guess with a convertible you could enter/exit Like Bo and Luke Duke.