I have heard of a Pertronix failing in the way you describe, causing misfires.
99% of the time when Pertronix fails, they just stop working entirely, but it could be the culprit here.
If you haven't already, you might try throwing a set of points on the car to see if that clears it up.
Aside from that, I would use a remote starter and engage the starter with the valve cover off to make sure all valves are opening and closing the way they should.
I doubt this is a carb issue from what you've described.
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